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366 [Rosetta] Input Handling minor unable to reproduce 2016-04-28 18:36 2016-04-28 18:36
rmoretti  
 
normal  
new  
open  
none    
none  
   
docking
n/a
Centroid mode docking doesn't work with Nucleic Acids?
Forum links:
https://www.rosettacommons.org/content/no-output-pdb-files-after-docking-protein-and-dnarna [^]
https://www.rosettacommons.org/node/9603 [^]

Apparently, there is/was an issue with using the docking protocol with nucleic acids, as the centroid mode docking code and centroid mode scoring has a bunch of "if (rsd.is_protein())" checks.

I (Rocco) have not personally checked this, I'm just forwarding a bug from the forums so it doesn't get lost. Note that the second forum post links to a (non-RosettaCommons lab) paper which contains a patch for protein/nucleic acid docking
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365 [Rosetta] Crash minor always 2016-04-28 16:59 2016-04-28 16:59
rmoretti  
 
normal  
new  
open  
none    
none  
   
all
n/a
Centroid mode doesn't work reliably for hydroxylproline
See https://www.rosettacommons.org/content/creating-centroid-patches-proline-prohydroxylatedcase1-and-prohydroxylatedcase2 [^]

I'm opening the bug to record the suggested fix:

> Line 0000002 of the pro_hydroxylated_case1.txt and pro_hydroxylated_case2.txt
> files located in /centroid/patches reads "TYPES HYDROXYLATION".
> Presumably, this is incorrect. It should be "TYPES HYDROXYLATION1" for
> pro_hydroxylated_case1.txt and "TYPES HYDROXYLATION2" for
> pro_hydroxylated_case2.txt.
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364 [Rosetta] Crash crash always 2016-04-12 14:13 2016-04-12 14:15
Labonte All platforms  
Any  
normal Any  
new Trunk  
open  
none    
none  
   
See above.
See above.
Confirmed As Bug
C-terminal_conjugation patch crashes several unit tests
When the C-terminal_conjugation patch is available to Rosetta, 13 unit tests fail, some of them crashing and all having to do with packing &/or rotamer-generation, from the following suites:

AACompositionEnergyTests
MirrorSymmetricConformationTests
AntibodyTaskOps
ConsensusLoopDesignOperationTests
DDGScan
RestrictOperationsTests

See also: https://github.com/RosettaCommons/main/pull/1259 [^]
Uncomment C-terminal_conjugation.txt from patches.txt and run the unit tests.
Andy guesses: "One of the interesting things is how in those tests that just make an all alanine or glycine pose and then build either alanine or glycine rotamers on it, we get 18 instead of 16. I bet the issue is that it's building a C-term conjugation rotamer on the C-term of that peptide--because it's missing its terminal atoms anyway?--and something is preventing variant matching from preventing it... or something."
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363 [Rosetta] Bad Coding minor always 2016-03-29 12:19 2016-03-29 12:19
smlewis All platforms  
Any  
low Any  
new All  
open  
none    
none  
   
unknown
irrelevant
rogue PDB output in core/scoring/packing/PoseBalls.cc
"rogue PDB output located in core/scoring/packing/PoseBalls.cc

it puts, uh, the balls in the PDB output. so I guess they should be appended sorta the way MEM or orbitals are, like ATOM records."

(From Andy W)
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361 [Rosetta] Bad Coding minor always 2015-09-28 12:26 2015-09-28 12:26
nannemdp MacBook Pro  
OSX  
normal 10.10.3  
new Trunk  
open  
none    
none  
   
rosetta_scripts, maybe others
rosetta_src_2015.05.57576_bundle/main/source/bin/rosetta_scripts.default.macosclangrelease @bug_example.flags -parser:protocol bug_example.xml -s 1UBQ_clean.pdb -nstruct 3
accumulation of REMARK output in packRotamersMover when nstruct>1
The PackRotamersMover tracks and writes to the output pdb the residues which are packed or designed using REMARK lines.
When nstruct > 1 the REMARK lines which track packable and designable residues and write out to the output pdb accumulate. So, if you use the PackRotamersMover 3 times then the number of REMARK lines is 3 times the number of decoys generated by the currently running process.

The issue tracks to PackRotamersMover::note_packertask_settings. Bug identified in 2015.05.57576 but code has not changed since 2011.
issue identified while using RosettaScripts. Files attached to reproduce.
Apparently you can only upload 1 file.....

FLAGS FILE
-database rosetta_src_2015.05.57576_bundle/main/database

-ndruns 2
-jd2:ntrials 100
-run:timer

-ex1
-ex2
-use_input_sc
-talaris2014

-options:user
-run:version

-chemical:exclude_patches LowerDNA UpperDNA Cterm_amidation SpecialRotamer protein_cutpoint_upper protein_cutpoint_lower VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm

-out:pdb_gz
#-mute all

-run:multiple_processes_writing_to_one_directory


RS XML FILE
<ROSETTASCRIPTS>
    <SCOREFXNS>
        <talaris2014 weights=talaris2014.wts />
    </SCOREFXNS>
    <TASKOPERATIONS>
        <RestrictToRepacking name=repackonly />
        <InitializeFromCommandline name=ifcl />
        <IncludeCurrent name=ic />
        <ReadResfile name=rrf filename="bug_example.resfile" />
    </TASKOPERATIONS>
    <FILTERS>
    </FILTERS>
    <MOVERS>
        <PackRotamersMover name=rp scorefxn=talaris2014 task_operations=rrf,ifcl,ic />
        
        <ParsedProtocol name=multi_rp >
            <Add mover=rp />
            <Add mover=rp />
            <Add mover=rp />
        </ParsedProtocol>
        
    </MOVERS>
    <APPLY_TO_POSE>
    </APPLY_TO_POSE>
    <OUTPUT scorefxn=talaris2014 />
    <PROTOCOLS>
        <Add mover_name=multi_rp />
    </PROTOCOLS>
</ROSETTASCRIPTS>

RESFILE bug_example.resfile
NATRO
start
1 A NATAA
2 A NATAA
3 A NATAA
4 A NATAA
5 A NATAA
6 A NATAA
7 A NATAA
8 A NATAA
9 A NATAA
10 A ALLAAxc
11 A ALLAAxc
12 A ALLAAxc
13 A ALLAAxc
14 A ALLAAxc
15 A ALLAAxc
16 A ALLAAxc
17 A ALLAAxc
1UBQ_clean.pdb (48,762) 2015-09-28 12:26
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=48&type=bug
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View Issue Details
190 [Rosetta] Bad Coding major always 2013-03-01 10:57 2015-08-18 11:13
smlewis  
 
normal  
new  
open  
none    
none  
   
all jd2
jd2memtest -l pdblist, where pdblist is large - watch the memory usage climb
-jd2:delete_old_poses and JD2 memory leak
JD2 has a longstanding memory leak that becomes quite serious in a large -l environment. "Old poses" - inputs that Rosetta is through with and will not reuse - are maintained in memory.

The flag -jd2:delete_old_poses prevents this memory leak but affects Oliver's code for reloading results into the JobDistributor as new jobs, and may affect RosettaScripts due to modification of Poses before distribution starts.
We'd love to turn the flag on by default, so that Rosetta does not leak memory. What code will have a problem with this, and can this code be run with -jd2:delete_old_poses false, or be fixed directly?

A) Oliver's code?
B) RosettaScripts?
Notes
(0000358)
jadolfbr   
2015-08-18 03:00   
Did we flip the switch on this at one of the dev meetings?
(0000360)
smlewis   
2015-08-18 11:13   
https://github.com/RosettaCommons/main/blob/master/source/src/basic/options/options_rosetta.py#L1140 [^]

nope





View Issue Details
7 [Rosetta] Crash minor always 2012-06-19 11:21 2015-08-18 03:07
smlewis All platforms  
Any  
low Any  
confirmed Trunk  
open  
none    
none  
   
all
rosetta -l pdblist @options
passing PDBs to -l causes unexpected behavior
If you pass a PDB to -l instead of to -s, Rosetta accumulates gobs of memory (10GB+) before your sysadmin gets mad and kills the job. It would be useful to track down why it is doing this...
instead of "ls *pdb > pdblist" and "rosetta -l pdblist", accidentally do "cat *pdb > pdblist" and "rosetta -l pdblist" and watch in horror as rosetta explodes in memory usage
Select this if your bug report applies to any platform.
Notes
(0000359)
jadolfbr   
2015-08-18 03:07   
This may be a duplicate of bug 190:

https://carbon.structbio.vanderbilt.edu/mantisbt/view.php?id=190 [^]





View Issue Details
359 [Rosetta] Incorrect Results minor always 2015-06-09 16:39 2015-08-18 00:53
jadolfbr All platforms  
jadolfbr Any  
low Any  
resolved Trunk  
fixed  
none    
none Trunk  
   
RS Features Output/ All output using databases
rosetta_scripts.linuxclangrelease -check_cdr_chainbreaks false -check_cdr_pep_bond_geom false -database $ROSETTA3/database -parser:protocol $1 @ features/features.flag -l $lambda $kappa -in:path $dir -out:path:all $out_dir -parser:script_vars name=$name s
Feature Request
58057
out:path:all does not work for features/database output
out:path:all works for score files and PDBs, but not features databases. The new databases always go to the current working directory.
Select this if your bug report applies to any platform.
Notes
(0000354)
jadolfbr   
2015-08-18 00:53   
Merge pull request #688 from RosettaCommons/jadolfbr/db_with_path
https://github.com/RosettaCommons/main/commit/63cc95ac7277ad06437162749bfa97a6a5b0b3e0?w=1 [^]

Allow pathing to database output

This merge allows -out:path:all to be used by -out:use_database and the FeaturesReporter framework. Adds another option -out:path:db to be used specifically for databases.

Tested using pdb output to db via score_jd2 and a feature reporter script.
Fixes bug/feature request 359: https://carbon.structbio.vanderbilt.edu/mantisbt/view.php?id=359 [^]





View Issue Details
140 [Rosetta] Incorrect Results minor sometimes 2012-10-20 10:42 2015-07-14 09:50
smlewis  
Labonte  
normal  
assigned  
open  
none    
none  
   
FoldTree, so all
--
FoldTree::reorder fails to reorder perfectly good fold trees
FoldTree::reorder fails to reorder perfectly good fold trees sometimes. I can't tell if there's a legitimate reason they can't be reordered, or if the function is just failing. There are a few reorder failures in the integration tests (all in my UBQ_E2 code), but they seem not to be a problem (it is failing to reorder(1) when root was already 1).

There is a code snippet as of SVN +-51727 in test/core/kinematics/FoldTree.cxxtest.hh that shows a perfectly good FoldTree that reorder fails on:

        std::istringstream reusable_FT_istream;

        //Test complex case 0000002 (stolen from UBQ_E2_thioester_extra_bodies integration test)
        core::kinematics::FoldTree UBQ_E2_fold_tree;
        reusable_FT_istream.clear();
        reusable_FT_istream.str("FOLD_TREE EDGE 1 173 -1 EDGE 85 249 -2 SG C EDGE 249 174 -1 JEDGE 249 297 1 C NZ END EDGE 297 325 -1 EDGE 297 250 -1 JEDGE 1 326 2 N N END EDGE 326 691 -1 JEDGE 1 692 3 N N END EDGE 692 779 -1");
        reusable_FT_istream >> UBQ_E2_fold_tree;

        UBQ_E2_fold_tree.reorder(UBQ_E2_fold_tree.root());
        //This results in this output:
        // core.kinematics.FoldTree: FoldTree::reorder( 1 ) failed, new/old edge_list_ size mismatch
        // core.kinematics.FoldTree: 10 5
        // core.kinematics.FoldTree: FOLD_TREE EDGE 1 173 -1 EDGE 85 249 -2 EDGE 249 174 -1 JEDGE 249 297 1 C NZ END EDGE 297 325 -1 EDGE 297 250 -1 JEDGE 1 326 2 N N END EDGE 326 691 -1 JEDGE 1 692 3 N N END EDGE 692 779 -1
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360 [Rosetta] Incorrect Results minor sometimes 2015-06-18 00:26 2015-06-18 00:26
jwillis0720 x86  
Linux  
normal Ubuntu  
new Trunk  
open  
none    
none  
   
rosetta_scripts
rosetta_scripts -s pdb.pdb -parser:protocol features.xml -database_partition 1
database sqlite output options don't do anything if using features reporter in rosetta scripts
-database_partition <int> does not append the database name nor create a partitioned schema. However, the tag in the xml

<ReportToDB name=features database_partition=<int>>

does produce a paritioned schema
Run rosetta_scripts using the -database_parition option instead of the xml tag and
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358 [Rosetta] Incorrect Results major always 2015-03-09 19:35 2015-03-09 19:35
AndrewLeaverFay All platforms  
AndrewLeaverFay Any  
normal Any  
assigned Trunk  
open  
none    
none  
   
all
/nas02/home/l/e/leaverfa/GIT/main/source/bin/optE_parallel.mpi.linuxgccrelease @optE_seqprof.flags @score.flags
new etables keep being created in optE
OptE started chewing up a lot of memory when the analytic etable was not being used; a quick bit of cout debugging showed that a new etable was getting created for each design job. Something fishy is going on in the way etables are retrieved from the scoring manager. The likely culprit is the EtableOptions::operator ==.
Run optE with the restore_pre_talaris_2013_behavior flag; it'll chew up memory in a few iterations.
$ cat score.flags
-database /nas02/home/l/e/leaverfa/GIT/main/database
-restore_pre_talaris_2013_behavior
-fa_max_dis 6.0
-score::bonded_params 300 150 40 40 40
-scale_d 1
-scale_theta 1
-scale_rb 1

...

$ cat optE_seqprof.flags
-s /nas02/home/l/e/leaverfa/optE/input_files/jsr55/interlaced_jsr54.list
-optE::optimize_nat_aa
-ignore_unrecognized_res
-mute all
# -ex1
# -ex2
-linmem_ig 10
-optE:free free_wts.txt
-optE:fixed fixed_wts.txt
-unmute protocols.optimize_weights.IterativeOptEDriver core.pack.min_pack core.init core.scoring.etable
-no_optH true
-skip_set_reasonable_fold_tree
-optimize_starting_free_weights
-mpi_weight_minimization
-optE:fit_reference_energies_to_aa_profile_recovery
#-optE::design_with_minpack # use regular linmem-ig redesign
-starting_refEs score12prime.wts
-optE:no_design_pdb_output
-n_design_cycles 12
-mpi_tracer_to_file testing
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353 [Rosetta] Bad Coding minor always 2014-10-06 18:15 2014-11-28 15:18
rmoretti  
 
normal  
new  
open  
none    
none  
   
JD2
various
"did you forget to pass -overwrite?" printed even if no jobs are considered.
In JD2, the "did you forget to pass -overwrite?" help message is printed even in cases where it wouldn't actually do anything - for example, if there weren't any jobs even considered.
Notes
(0000353)
pconerly   
2014-11-28 15:18   
This comes from `/main/source/src/protocols/jd2/JobDistributor.cc`, line 658, it's from checking the `tried_jobs` variable as oppose to checking a hypothetical `jobs_given` variable.

(I'm still learning the codebase and I'm not sure what the entrypoint is to repro this bug.)





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357 [Rosetta] Bad Coding minor always 2014-11-13 10:49 2014-11-21 08:31
AndrewLeaverFay  
stoneinter  
normal  
assigned Trunk  
open  
none    
none  
   
everything
dummy_command_line
Confirmed As Bug
Lei Shi has duplicated almost the entirety of BackboneStubConstraint in creating BackboneStubLinearConstraint
Code duplication.
Lei Shi needs to create an account on Mantis so that I can assign him this bug. If you are in the Baker lab, stop by his desk and let him know that I created this bug, please.
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356 [Rosetta] Crash minor always 2014-11-04 11:12 2014-11-04 11:12
rmoretti  
 
normal  
new  
open  
none    
none  
   
minirosetta
minirosetta.linuxgccrelease @options
Minirosetta threading protocol segfaults on alignments with no gap.
If you use the threading protocol on the minirosetta application with an alignment which doesn't have any gaps, Rosetta will segfault. The error occurs in protocols::loops::fold_tree_from_loops(), where root() is taken from an empty FoldTree. The reason for the empty FoldTree is that the loops passed in is empty, because in LoopRelaxMover::apply(), pick_loops_chainbreak() returns no loops.
One fix may be to turn off loop refinement as well as loop remodeling in the test for an empty loop return from pick_loops_chainbreak().

fold_tree_from_loops() should probably be robust to an empty loops - or at the very least shouldn't segfault.

See https://www.rosettacommons.org/comment/7926 [^]
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355 [Rosetta] Bad Coding minor always 2014-11-03 18:01 2014-11-03 18:01
rmoretti  
 
normal  
new  
open  
none    
none  
   
backrub
na
backrub application and JD2 integration
The backrub application was converted to JD2, but doesn't take advantage of the JD2 output features, making it difficult to target alternative output formats (e.g. silent files). Additionally, the output structure that is chosen is the lowest energy structure, when the common usage of backrub apparently makes use of the last structure instead.

It might be nice to use the auxiliary output handling of JD2 to deal with the output of the lowest energy structure in addition to the output of the last structure by the common route.
See https://www.rosettacommons.org/node/3854 [^]
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354 [Rosetta] Incorrect Results minor always 2014-10-21 12:58 2014-10-21 12:58
jadolfbr All platforms  
Any  
normal Any  
new Trunk  
open  
none    
none  
   
Antibody modeling suite - antibody.py script application, ROSIE
ROSIE antibody modeling
Missing residues from ROSIE antibody modeling
A user used the antibody modeling apps through ROSIE and had two residues missing in the final antibody structure.

https://www.rosettacommons.org/node/3769 [^]

From conversations with people more knowledgeable than I in regards to the antibody suite, it most likely has to do with the framework that was chosen from the input sequence.

In cases like these, the antibody modeling script could call the partial_thread application and then the hybridize comparative modeling application to create the full structure of the antibody without the CDRs. This may be difficult as hybridize may try to connect the CDR stems. Perhaps a call to Remodel would be sufficient to add the missing residues.
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350 [Rosetta] Crash minor always 2014-09-22 11:41 2014-09-22 11:41
rmoretti  
 
normal  
new  
open  
none    
none  
   
fragment picker
fragment picker -s SPI.pdb
Fragment Picker SegFaults when not given a sequence
Report from Forum post (https://www.rosettacommons.org/node/3797 [^])

A user tried to run fragment picking by using the "-s" option with a PDB, rather than using any of the sequence input options. This resulted in a segfault in protocols::frag_picker::scores::MakeSecondarySimilarity::make(), presumably when FragmentPicker::get_query_seq() is called, returns a null OP, and is dereferenced.
(I have not reproduced this with trunk - it may have been addressed already, although I didn't notice anything.)
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349 [PyRosetta] Bad Coding minor always 2014-08-04 15:55 2014-08-13 13:02
rmoretti  
Sergey  
normal  
resolved  
fixed  
none    
none  
   
BuildBindings.py
na
57188
Linux versioning issue with PyRosetta BuildBindings.py
When getting the version of Linux BuildBindings.py apparently assumes a single digit point release:

lib_path = 'build/src/'+mode+'/linux/' + platform.release()[:3] + '/' + PlatformBits +'/x86/gcc/'"

This causes a mismatch issue with scons's version parsing.
See the forum post at https://www.rosettacommons.org/node/3758 [^] for more information.
Notes
(0000352)
Sergey   
2014-08-13 13:01   
Fixed in master:57188





View Issue Details
347 [Rosetta] Bad Coding minor always 2014-07-30 01:13 2014-07-30 01:13
hajosep All platforms  
momeara Any  
low Any  
assigned All  
open  
none    
none  
   
Scientific BenchMarking
ProteinResidueConformation Features
Feature Request
Seqpos in ProteinResidueConformation
Most of the features reporter use resNum to define the Rosetta numbering of amino acids in a pdb; however ProteinResidueConformation uses seqpos. Ideally this nomenclature should be consistent.
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345 [Rosetta] Incorrect Results major always 2014-07-03 12:39 2014-07-29 16:37
Labonte All platforms  
Labonte Any  
high Any  
resolved Trunk  
fixed  
none    
none Trunk  
   
anything using CCD closure
N/A
Confirmed As Bug
57131
The rama score check in CCD closure behaves exactly opposite the way it should.
If the rama check flag is set to true during CCD closures, the moves are always accepted if the rama check score is WORSE!
Offending code:
// evaluate the rama score difference:
Real const old_rama_score( rama->eval_rama_score_residue( pose.aa(pos), torsions[pos][1], torsions[pos][2]));
Real const new_rama_score( rama->eval_rama_score_residue( pose.aa(pos), save_torsions[1], save_torsions[2]));

if (local_verbose)
tccd.Warning << "rama_check_boltzmann: " << pos << ' ' << old_rama_score << ' ' << new_rama_score << std::endl;

if ( new_rama_score > old_rama_score ) {
Real const boltz_factor ( (old_rama_score-new_rama_score)/ccd_temperature );
Real const negative_forty( -40.0f );
Real const probability ( std::exp(std::max(negative_forty,boltz_factor) ) );
if ( new_rama_score - start_rama_score[ pos ] > max_rama_score_increase ||
numeric::random::uniform() >= probability ) {
// undo the change:
torsions[pos] = save_torsions;

// recover saved coords
for ( int i=loop_begin; i<= loop_end; ++i ) {
for ( Size j=1; j<= nbb; ++j ) {
coords[i][j] = save_coords[i][j];
}
}

get_overlap_pos( coords, torsions, cutpoint, direction, bond_angle1, bond_length, bond_angle2, M );

} // rama reject
} // rama-score got worse
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39 [Rosetta] Input Handling crash always 2012-07-05 10:03 2014-07-19 13:50
tjacobs2  
rmoretti  
normal  
resolved  
fixed  
none    
none  
   
Docking
rosetta_source/bin/rosetta_scripts.mpipostgres.linuxgccrelease -s single_chain.pdb -docking:dock_pert 2 4
68a25f6cf54d946afe86786bdab4c81dd9cfd0a8
Running docking on a single-chain PDB causes a segfault
Running docking on a single-chain PDB causes a segfault
Run the docking script (pasted in additional information) on a PDB with only a single chain. Await segfault
RosettaScripts protocol:

<ROSETTASCRIPTS>
        <SCOREFXNS>
      <s12_prime weights="score12prime"/>
        </SCOREFXNS>
    <TASKOPERATIONS>
      <RestrictToInterfaceVector name=vectorTask chain1_num=1 chain2_num=2 CB_dist_cutoff=10.0 nearby_atom_cutoff=5.5 vector_angle_cutoff=65.0 vector_dist_cutoff=8.0/>
      <RestrictChainToRepacking name=repack1 chain=1/>
      <RestrictChainToRepacking name=repack2 chain=2/>
      <RestrictToRepacking name=repackonly/>
      <InitializeFromCommandline name=cmdTask/>
      <IncludeCurrent name=currentTask/>
        </TASKOPERATIONS>
        <FILTERS>
      <Rmsd name=rms threshold=50.0 confidence=1/>
    </FILTERS>
        <MOVERS>
      <Prepack name=prepack scorefxn=s12_prime jump_number=1 min_bb=0 task_operations=vectorTask,repackonly,cmdTask,currentTask/>
      <DockingProtocol name=dockprotocol docking_local_refine=1 docking_score_high=s12_prime ignore_default_docking_task=1 task_operations=vectorTask,repack1,repack2,cmdTask,currentTask/>
      <TaskAwareMinMover name=minmover scorefxn=s12_prime chi=1 bb=1 jump=1 task_operations=vectorTask,cmdTask,currentTask/>
      <InterfaceAnalyzerMover name=fullanalyze scorefxn=s12_prime packstat=1 pack_input=0 jump=1 tracer=0 use_jobname=1 resfile=0 />
        </MOVERS>
        <APPLY_TO_POSE>
        </APPLY_TO_POSE>
        <PROTOCOLS>
      <Add mover_name=prepack/>
      <Add mover_name=dockprotocol filter_name=rms/>
      <Add mover_name=minmover filter_name=rms/>
      <Add mover_name=fullanalyze/>
        </PROTOCOLS>
</ROSETTASCRIPTS>
Notes
(0000351)
rmoretti   
2014-07-19 13:50   
Segfault was due to attempting to find an interface between two chains that don't exist. Catch and utility exit instead.





View Issue Details
332 [Rosetta] Bad Coding minor sometimes 2014-04-17 09:55 2014-07-19 13:23
rmoretti  
rmoretti  
normal  
resolved  
fixed  
none    
none  
   
scons
scons.py mode=release bin
aa7b53799ffbe6b
Problems compiling with uint64_t
On some platforms it appears that the definition of uint64_t is missing/faulty.
This expresses itself as a compilation error in src/protocols/wum2/EndPoint.cc:

src/protocols/wum2/EndPoint.cc:21:42: error: a function call cannot appear in a constant-expression

If you supplement the definition of uint64_t with the one defined by boost/cstdint.hpp this apparently fixes the error.
Try compiling on an affected platform.
Forum thread reporting the issue: https://www.rosettacommons.org/node/3582 [^]

Notes
(0000341)
rmoretti   
2014-04-17 11:29   
Andrew let me know that uint64_t usage in Rosetta is mostly boost based, and looking at src/protocols/wum2/EndPoint.hh I now see a "using namespace boost" line. The fix here is probably to get rid of the using declaration in the header and be explicit about using the boost version of uint64_t.

(There's a complication in all of this that uint64_t is available under C++11, but only for platforms where it's a native type. E.g. not for 32-bit compilers, which may be why there's such a platform dependent muddle.)
(0000342)
Sergey   
2014-04-18 14:41   
(edited on: 2014-04-18 14:42)
Rocco, types like uint64_t should not be really used anywhere besides platform/*. Could this be replaced with core::Size? (using uint64_t directly would create numerous problem for Windows build as well)

(0000343)
rmoretti   
2014-04-21 09:05   
Andrew said that he's used the boost::uint64_t and the like when he's needed a type that's specifically 64 bits long. I would assume that the boost library should figure out all the cross platform issues such that explicit use of the boost::uint64_t wouldn't have compilation issues on Windows, but I'm not certain of that.





View Issue Details
278 [Rosetta] Input Handling minor always 2013-05-31 10:03 2014-07-19 10:55
smlewis  
rmoretti  
normal  
resolved 3.4  
fixed  
none    
none  
   
docking in particular, anything with fullatom/centroid mode and constraints
-cst_file file_with_atompairconstraints
???
AtomPairConstraint does not check existence of atoms (?)
This is a bug I've run into in old versions of Rosetta (3.4 and earlier). A casual reading of trunk suggests this has been fixed but we need to check it.

AtomPairConstraint does not appear to check if atoms actually exist before attempting to apply constraints. If you pass fullatom constraints into centroid mode, where the sidechain atoms do not exist, the constraint functions look at garbage atom positions and return garbage constraint scores. Occasional crashes occur from segfaults, but usually it looks at allocated but inappropriate memory.

Here's a 3.4 example. https://www.rosettacommons.org/node/3278 [^]

I have not yet attempted to reproduce this in trunk.
Notes
(0000313)
amw579   
2013-08-15 10:02   
OK, do you mean that this _only_ happens when the reason the atoms don't exist is because of centroid mode? Or are you concerned that this is a general failure mode when atoms don't exist?

It's definitely not true in the general case--just weeks ago I was dinged for constraining nonexistent atoms--but maybe it's somehow a specific-to-centroid-mode problem.
(0000350)
rmoretti   
2014-07-19 10:54   
It's definitely been fixed by 2013wk52. This has been tested with centroid poses & sidechain constraints.

AtomPairConstraint used core::pose::named_atom_id_to_atom_id(), which checks for existence and raises EXCN_AtomNotFound if the atom is not found.





View Issue Details
346 [Rosetta] Crash minor always 2014-07-07 14:11 2014-07-07 14:12
rmoretti  
 
normal  
new  
open  
none    
none  
   
InterfaceAnalyzer
InterfaceAnalyzer.linuxgccrelease -fixedchains A B -compute_packstat -no_nstruct_label -out:file:score_only interface_analysis.sc -s *.pdb.gz -extra_res_fa XTRA101.params
Using IntefaceAnalyzer with a ligand and -fixedchains results in segfault
In a two-protein, one small molecule ligand protein, using the -fixedchains option (either with "-fixedchains A B" or "-fixedchains X") results in a Segfault. This is likely due to the single residue peptide edge made in the foldtree:

apps.public.analysis.InterfaceAnalyzer: Fixed chains are: A, B, these will be moved together.
core.kinematics.FoldTree: FoldTree::reorder( 287 ) failed, new/old edge_list_ size mismatch
core.kinematics.FoldTree: 5 4
core.kinematics.FoldTree: FOLD_TREE EDGE 1 234 -1 EDGE 1 287 1 EDGE 235 286 -1 EDGE 235 234 2 EDGE 287 287 -1
Segmentation fault
FXAX_gtc000398_XTRA101_0001.pdb.gz (91,206) 2014-07-07 14:11
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=45&type=bug
XTRA101.params (6,513) 2014-07-07 14:12
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=46&type=bug
There are no notes attached to this issue.





View Issue Details
343 [Rosetta] Input Handling minor always 2014-06-26 14:11 2014-06-26 14:46
jadolfbr All platforms  
jadolfbr Any  
low Any  
assigned Trunk  
open  
none    
none  
   
All
antibody_designer.linuxclangrelease -in:path antibody_designer @flags
Options file do not use -in:path directory locations
Options file loading should use set paths for locating files.
Use a cmd line where your flags file is in a different directory; pass -in:path to that directory
Select this if your bug report applies to any platform.
Notes
(0000349)
rmoretti   
2014-06-26 14:46   
This is a little cart-before-the-horse, as you would need to be able to use the option system before/when you're actually loading the options.

I guess it might be possible, so long as you specify -in:path on the command line before you specify the options file (so "antibody_designer.linuxclangrelease -in:path antibody_designer @flags" might be workable, "antibody_designer.linuxclangrelease @flags -in:path antibody_designer" wouldn't be, at least without changing options loading semantics.)

To make the first case work, you'd probably have to alter OptionCollection::load_option_from_file() in src/utility/options/OptionCollection.cc to specifically introspect the -in:path option and uses those paths as fallbacks. The general -in:path loading mechanism that usually happens through izstream won't work, as that doesn't get set until the options loading is finished.





View Issue Details
342 [Rosetta] Input Handling minor always 2014-06-25 13:25 2014-06-25 13:25
jadolfbr All platforms  
Any  
low Any  
new  
open  
none    
none  
   
compare_sample_sources.R
./compare_sample_sources.R --config local_json.json
Features scripts hardcode ref as the first sample_source
Although you can specify reference = true or false in the json for controlling which db is the reference, in the R features framework this is hardcoded as the first database of sample_sources.
Use a script that requires a reference database and pass the reference database as not-the-first on the list
See query_sample_sources_as_ref function in methods.R
Select this if your bug report applies to any platform.
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View Issue Details
341 [Rosetta] Bad Coding minor always 2014-06-24 16:29 2014-06-24 16:30
rmoretti  
 
normal  
new  
open  
none    
none  
   
na
na
Too many add_cutpoint/chainbreak_variants functions
As mentioned by Justin in bug 0000336, we have a number of different "add chainbreak variants to pose" functions:

core::pose::correctly_add_cutpoint_variants
protocols::forge::methods::add_cutpoint_variants
protocols::loops::loops_main::add_cutpoint_variants
protocols::abinitio::add_chainbreak_variants
protocols::environment::add_chainbreak_variants
protocols::topology_broker::add_chainbreak_variants

These functions (and any corresponding remove_* or has_* functions), should likely be consolidated.
For preference, I'd say that we should consolidate under the core::pose namespace, as adding the cutpoints is a general pose manipulation.

Once successfully accomplished, the function probably should be renamed to just "add_cutpoint_variants". (We can't do that just yet, due to Koenig lookup issues.)

Complications noticed so far is how to normalize differences in error handling - e.g. what if a location isn't a chainbreak in the fold tree? Do you raise an error or silently pass? How about if they're already an incompatible termini ending - again raise an error or pass silently.

Another issue is side manipulations: The protocols::loops version does constraint remapping. That should probably be added to the centralized version, but I'm thinking we might instead want to make that a more general property of adding/removing variant types. That is, have the pose introspect about residue type changes and update associated data appropriately.
There are no notes attached to this issue.





View Issue Details
336 [Rosetta] Bad Coding minor always 2014-06-06 08:54 2014-06-24 16:30
rmoretti  
rmoretti  
normal  
resolved  
fixed  
none    
none  
   
na
na
Confirmed As Bug
56982
core::util::add_cutpoint_variants() and remove_cutpoint_variants() take raw pointers
Against coding conventions, core::util::add_cutpoint_variants() and remove_cutpoint_variants() take raw pointers to a Pose. They should be re-written to either take an owning pointer, or (preferably) a reference to a Pose
Notes
(0000346)
jrporter   
2014-06-06 09:24   
Removing the pointer should be easy to do, but while we're at it, we might also want to ask ourselves how this function differs from:

core::util::pose::correctly_add_cutpoint_variants
protocols::forge::methods::add_cutpoint_variants
protocols::loops::loops_main::add_cutpoint_variants
protocols::abinitio::add_chainbreak_variants
protocols::environment::add_chainbreak_variants
protocols::topology_broker::add_chainbreak_variants


In fairness, the last one is depricated and the penultimate is mine, but I'd love to get rid of them with some lower-level API call, if we can. I think we need to consider that not all fold tree cuts must necessarily be replaced with chainbreaks.
(0000348)
rmoretti   
2014-06-24 16:29   
The core of the issue (the raw pointers) has been addressed. The additional issue that Justin raised has been added as a new bug (0000341).





View Issue Details
337 [Rosetta] Bad Coding minor always 2014-06-09 10:22 2014-06-23 14:45
rmoretti  
rmoretti  
normal  
resolved  
fixed  
none    
none  
   
relax, score_jd2, others
many
56978
Spurious "WARNING: In CA_rmsd, residue range ... to ... requested but only ... protein CA atoms found." messages.
In things like relax, CA_rmsd(pose1,pose2) is called, which then calls CA_rmsd( pose1, pose2, start, end ) - The latter, with an explicit range, checks to make sure that every residue in the given range is used. If not, it prints a warning message.


This is sub-optimal for situations like relax, etc. which do the whole-structure rmsd, and may include non-protein residues like virtual residues or ligands, whose presence in the range is not really a warn-able offense.
We probably want to make the logic smarter, so that it only warns if you're missing from an explicitly given range, not if you're missing from the implicit "all the residues in the pose" range. (Combining the two function using default arguments may be the easiest way to do this cleanly.)

HT Justin Porter for pointing out this long-standing issue on the mailing list.
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View Issue Details
335 [Rosetta] Incorrect Results minor always 2014-06-03 12:33 2014-06-23 14:42
rmoretti  
rmoretti  
normal  
resolved Trunk  
fixed  
none    
none  
   
test/run.py
test/run.py -c clang --compiler_version 3.4
Confirmed As Bug
56977
test/run.py doesn't have version option
If you compile with scons cxx_ver=*, test/run.py isn't able to find the proper compiler directory, as it doesn't have a version option.

Adding a version option to the run.py script fixes the issue.
Probably should also fix the cxx=gcc default in the cxx option as well. (Setting default option equal to None seems to work as expected.)
There are no notes attached to this issue.





View Issue Details
340 [Rosetta] Input Handling minor always 2014-06-23 12:11 2014-06-23 12:11
rmoretti  
 
normal  
new  
open  
none    
none  
   
any
many
Printing of commandline removes quotes
If you provide a quoted commandline variable to Rosetta (for example, you use the property of -s that will concatenated PDB files), when it's printed in the log file it will become unquoted.

E.g. the command:

score_jd2.linuxgccrelease -s "protein.pdb ligand.pdb"

Will be printed as

core.init: command: score_jd2.linuxgccrelease -s protein.pdb ligand.pdb

in the log file. The commands with and without quotes have very different behaviors.
When printing, we should probably check for things like spaces, and if present add quotes to make things copy-pastable.
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View Issue Details
139 [Rosetta] Documentation minor always 2012-10-19 16:51 2014-06-16 11:08
kimdn  
rmoretti  
normal  
resolved  
fixed  
none    
none  
   
rosettacommons
http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d1/d97/resfiles.html [^]
trunk
near duplicate documentation - resfile
At

http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d1/d97/resfiles.html [^]

I see some duplicate documentations.
Notes
(0000347)
rmoretti   
2014-06-16 11:08   
At least as of transition to the documentation wiki, this duplication no longer occurs. (I believe it's also fixed in prior versions.)

Rosetta3.4 online documentation still has the duplication, but that's not something we're going to go back and correct.





View Issue Details
334 [Rosetta] Crash minor always 2014-05-26 11:47 2014-05-26 11:47
rmoretti  
 
normal  
new  
open  
none    
none  
   
homodimer_maker
homodimer_maker.linuxgccrelease -s 2a7b_mpm.pdb @maker_options
homodimer_maker (beta_strand_homodimer_design) does not work with talaris2013
Running the beta_strand_homodimer_design demo with a recent weekly release results in an error on the homodimer_maker step:

ERROR: homodimer_maker is incompatible with analytic_etable_evaluation. Please either fix the code or add '-analytic_etable_evalution 0' to the command line.
Run the beta_strand_homodimer_design demo.
From forum thread: https://www.rosettacommons.org/node/3692 [^]
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View Issue Details
167 [Rosetta] Website error minor always 2012-12-21 09:04 2014-05-17 10:02
smlewis  
rmoretti  
normal  
resolved  
fixed  
none    
none  
   
website
website
na
Website error: software link on software page 404's; also new bug category test
Bug:
1. Go to the Software page.
2. Try to click the Software link from this page.
3. Goes to a 404 page, wrong link.
Notes
(0000345)
rmoretti   
2014-05-17 10:02   
We have a new website, and all the links on the site seem to be working now.





View Issue Details
185 [Rosetta] Bad Coding minor always 2013-03-01 09:05 2014-05-17 09:59
smlewis All platforms  
smlewis Any  
low Any  
resolved  
fixed  
none    
none  
   
integration tests, integration3.py integration.py
integration3.py
trunk
Is integration3.py deprecated?
Is integration3.py deprecated? We used it in our lab until Sergey fixed bugs 0000033, 0000026. We don't want integration.py and integration3.py to drift apart...
Select this if your bug report applies to any platform.
Notes
(0000158)
rmoretti   
2013-03-04 12:47   
Consensus on the rosetta-devel mailing list as of 1-Mar-2013 was that integration3.py was now redundant, and should be removed.

There was also some discussion regarding supporting both Python2 and Python3 in a single script, or a single core script that dynamically loads auxiliary functions based on the version of Python used.
(0000159)
smlewis   
2013-03-04 15:20   
54053 addresses this bug by disabling and deprecating integration3. If nobody objects within a month or so, integration3 can be deleted.
(0000344)
rmoretti   
2014-05-17 09:59   
integration3.py has been removed by parties unknown.





View Issue Details
331 [Rosetta] Input Handling minor always 2014-04-08 12:46 2014-04-08 12:46
rmoretti  
 
normal  
new  
open  
none    
none  
   
all
score_jd2.linuxgccdebug -s *.pdb
Confirmed As Bug
Missing backbone and TER cards result in errors.
If there's a residue with missing backbone atoms in the first residue after a TER card, Rosetta will halt with the error:

ERROR: Can't create a polymer bond after residue 4 due to incompatible type: ILE_p:CtermProteinFull
ERROR:: Exit from: /hd0/morettr/Rosetta/main/source/src/core/conformation/Conformation.cc line: 628
Error: ERROR: Exception caught by JobDistributor while trying to get pose from job 'doesntwork_0001'
Error:
[ERROR] EXCN_utility_exit has been thrown from: /hd0/morettr/Rosetta/main/source/src/core/conformation/Conformation.cc line: 628
ERROR: Can't create a polymer bond after residue 4 due to incompatible type: ILE_p:CtermProteinFull


Removing either the TER card or removing the missing atoms gives results as one expects.
Load the attached file into Rosetta
doesntwork.pdb (3,001) 2014-04-08 12:46
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=44&type=bug
There are no notes attached to this issue.





View Issue Details
328 [Rosetta] Input Handling minor always 2014-03-27 10:57 2014-03-27 10:57
rmoretti  
 
normal  
new  
open  
none    
none  
   
all
na
Ligands will all atoms incorrectly named cause Rosetta error.
If you have a (non-polymeric) ligand in your PDB, but you don't have any of the appropriately named atoms, Rosetta will attempt to put the ligand in the pose (as opposed to discarding/ignoring it), but when it tries to fill the missing atoms it won't have anything to anchor on, so it will just spin helplessly until it errors out with a somewhat obtuse error message.
Take a structure with a non-polymeric ligand. Rename all the atoms in the PDB to something else. Try to score it in Rosetta.
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View Issue Details
327 [Rosetta] Bad Coding minor always 2014-03-17 16:57 2014-03-17 16:57
rmoretti  
 
normal  
new  
open  
none    
none  
   
rosetta_scripts
na
RmsdFilter doesn't work well with reference poses.
In protocols::protein_interface_design::filters::RmsdFilter, you can only do whole structural comparisons with a set reference pose. Any sub-structure limitations on the range of residues with which to calculate Rmsd are done at parse time, and the saved reference pose may not be properly initialized at parse time.
The parsing of relevant residues should likely be deferred until apply time, as the reference pose may change (or be).

Actually, it's probably better to extend the filter to use Andrew's new ResidueSelectors framework, as opposed to having an ad hoc specification system.
There are no notes attached to this issue.





View Issue Details
325 [Rosetta] Input Handling minor always 2014-02-26 15:35 2014-02-26 15:35
jadolfbr All platforms  
Any  
normal Any  
new Trunk  
open  
none    
none  
   
Many depending on context
rosetta_scripts.linuxclangrelease -database $ROSETTA3/database -parser:protocol LH_interface_general.xml @LH_interface_analysis.flag -l $dir/$ss/full_PDBLIST_heavy_culled.txt -parser:script_vars sep=$sep tog=$tog name=LH_Fv_repack_both.sasafix score=$scor
non-cannonical AA at terminal position causes incorrect chain identification
If loading a PDB with an ignored non-cannonical terminal residue, such as PCA, Rosetta will incorrectly identify the chain of the next set of residues, such that those residues will be a part of the previous chain. Foldtree is correctly identified. For example, a two chain pose will be one chain in Rosetta.
Load the file into PyRosetta with -ignore_unrecognized_res, query the number of chains in the pose.
PCA is pyrrolidone carboxylic acid. Removing this residue from the PDB file makes it load correctly.
Select this if your bug report applies to any platform.
3twcL-3twcH.pdb (238,922) 2014-02-26 15:35
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=41&type=bug
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View Issue Details
323 [Rosetta] Incorrect Results minor always 2014-02-04 10:41 2014-02-11 14:14
jadolfbr All platforms  
jadolfbr Any  
normal Any  
assigned Trunk  
open  
none    
none  
   
many
NA
scoring/sasa.hh reports values by default using radii that were optimized for a no-longer-used scoreterm
In the function calc_per_atom_sasa, 3 radii can be used for the calculation. These include the Rosetta default, LJ radii, and those from the program Naccess. The default is to use the Rosetta default - radii that were explicitly optimized for use in a scoreterm that is no longer used. I don't think the scoreterm was ported to Rosetta3.

This is fine, but many programs and classes (perhaps blindly) use these default radii and should probably use either the LJ or the standard Naccess radii instead as it seems using the Rosetta defaults can produce SASA values differing by 0000011:0000005-10% from LJ/Naccess values.
Use core/scoring/sasa/calc_per_atom_sasa using default setting. Or use the SasaCalculator pose metric. Even better, use pretty much any of the functions within sasa.hh that call calc_per_atom_sasa using default values.
Changing the defaults would change numerous pieces of Rosetta and I'm not sure I'm ready to do that. However, I have reorganized the code and commented it heavily so that this should be known. In reality, sasa.hh should probably be its own class either within core/scoring or as a simple mover with LJ or Naccess radii being the expected defaults.
Select this if your bug report applies to any platform.
Notes
(0000328)
jadolfbr   
2014-02-04 11:59   
In addition to this, using Naccess defaults with all atoms will result in the wrong values of SASA due to the Naccess radii being that from Chothia 1976 ('The Nature of the Accessible and Buried Surfaces in Proteins'):

"Hydrogen atoms were not considered individually but included in the van der Waals radii used for the non-hydrogen atoms. The van der Waals radii used, oxygen 1.4 A, trigonal nitrogen 1.65, tetrahedral nitrogen 1.5, tetrahedral carbon 1.87, trigonal carbon 1.76, sulphur 1.85, and water 1.4, were derived from the intermolecular contact distances observed between non-hydrogen atoms in crystals of amino acids"





View Issue Details
324 [Rosetta] Bad Coding major always 2014-02-04 10:50 2014-02-04 10:50
jadolfbr  
sacombs  
normal  
assigned Trunk  
open  
none    
none  
   
many
NA
ideal_bond_lengths.txt has values that are just plain wrong - these are used to build ideal geometry all over Rosetta
The description in database/atom_type_sets/fa_standard/ideal_bond_lengths.txt speaks for itself:

#bond lengths were determined by averaging bonds between atoms found in
#residue params files. All bonds not in params were assigned 1.54 and
#commented
Use any of the polymer building functions in core/conformation or any function/class that uses these (note how they almost always set use_ideal_geometry true).
It seems that Steven Combs is hard at work fixing this issue among many other residue/atom typing bugs.
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View Issue Details
322 [Rosetta] Bad Coding minor always 2014-01-23 08:25 2014-01-23 08:25
momeara All platforms  
weitzner Any  
normal Any  
assigned All  
open  
none    
none  
   
get_rosetta.sh
curl -O https://raw.github.com/RosettaCommons/rosetta_clone_tools/master/get_rosetta.sh [^] && bash get_rosetta.sh demos
Confirmed As Bug
when only checking out 1 repository, it still asks if you'd like to check out all three in parallel
the get_rosetta.sh script allows one to only check out a single repository, but it still asks if you'd like to check all three out in parallel.
curl -O https://raw.github.com/RosettaCommons/rosetta_clone_tools/master/get_rosetta.sh [^] && bash get_rosetta.sh demos
Select this if your bug report applies to any platform.
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View Issue Details
320 [Rosetta] Bad Coding minor always 2014-01-21 14:03 2014-01-21 14:20
Labonte  
Labonte  
normal  
resolved Trunk  
fixed  
none    
none Trunk  
   
unknown
-out:levels core.chemical.PatchOperations.hh:400
TBD
Patch system fails to patch SER properly in 158 cases
When the Tracer volume is turned up for core.chemical.PatchOperations.hh, it becomes clear that there are issues patching the SER ResidueType with the phosphorylated patch due to a missing HG atom.
Use the -out:levels core.chemical.PatchOperations.hh:400 flag.
Tracer Output:
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:NtermProteinFull_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:protein_cutpoint_upper_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_lower_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:protein_cutpoint_lower_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:ProteinVirtBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:NtermProteinFull_p:ProteinVirtBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:ProteinVirtBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:protein_cutpoint_upper_p:ProteinVirtBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_lower_p:ProteinVirtBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinVirtBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:protein_cutpoint_lower_p:ProteinVirtBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:NtermProteinFull_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:protein_cutpoint_upper_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_lower_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:protein_cutpoint_lower_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:NtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:protein_cutpoint_upper_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_lower_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:protein_cutpoint_lower_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:NtermProteinFull_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:NtermProteinFull_p:ProteinVirtBB_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinVirtBB_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinShoveBB_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:NtermProteinFull_p:ProteinShoveBB_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinShoveBB_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:NtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinVirtBB_p:ProteinShoveBB_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:Virtual_Protein_Residue_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_lower_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:protein_cutpoint_lower_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:ProteinVirtBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_lower_p:ProteinVirtBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinVirtBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:protein_cutpoint_lower_p:ProteinVirtBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_lower_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:protein_cutpoint_lower_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:ProteinVirtBB_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_lower_p:ProteinVirtBB_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinVirtBB_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:protein_cutpoint_lower_p:ProteinVirtBB_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:VirtualNterm_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:VirtualNterm_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:VirtualNterm_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinVirtBB_p:VirtualNterm_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinShoveBB_p:VirtualNterm_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinShoveBB_p:VirtualNterm_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:VirtualNterm_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinVirtBB_p:ProteinShoveBB_p:VirtualNterm_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:Virtual_Protein_Residue_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermConnect_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:CtermConnect_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinShoveBB_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:VirtualNterm_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:VirtualNterm_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinShoveBB_p:VirtualNterm_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:VirtualNterm_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:Virtual_Protein_Residue_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:VirtualNterm_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:VirtualNterm_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinShoveBB_p:VirtualNterm_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:VirtualNterm_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:Virtual_Protein_Residue_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermConnect_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:CtermConnect_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:phosphorylated_p:MethylatedCtermProteinFull is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:phosphorylated_p:MethylatedCtermProteinFull is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:phosphorylated_p:AcetylatedNtermProteinFull is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:phosphorylated_p:AcetylatedNtermProteinFull is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:phosphorylated_p:MethylatedCtermProteinFull_p:AcetylatedNtermProteinFull is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:phosphorylated_p:MethylatedCtermProteinFull_p:AcetylatedNtermProteinFull is missing atom: HG
Notes
(0000326)
Labonte   
2014-01-21 14:20   
Was a patching bug in my carbohydrate code, which I've fixed for my next push. It won't actually affect anyone not using the -include_sugars flag.





View Issue Details
309 [Rosetta] Bad Coding minor always 2013-10-25 13:22 2014-01-21 14:04
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-out:levels core.chemical.PatchOperations.hh:400
Patch system fails to patch HIS_D properly in 4 cases
When the Tracer volume is turned up for core.chemical.PatchOperations.hh, it becomes clear that there are issues patching the HIS_D ResidueType due to a missing HE2 atom.
Use the -out:levels core.chemical.PatchOperations.hh:400 flag.
Tracer Output:
core.chemical.PatchOperations.hh: SetAtomType::apply failed: HIS_D is missing atom: HE2
core.chemical.PatchOperations.hh: SetAtomType::apply failed: HIS_D_p:ProteinVirtBB is missing atom: HE2
core.chemical.PatchOperations.hh: SetAtomType::apply failed: HIS_D_p:ProteinShoveBB is missing atom: HE2
core.chemical.PatchOperations.hh: SetAtomType::apply failed: HIS_D_p:ProteinVirtBB_p:ProteinShoveBB is missing atom: HE2
Select this if your bug report applies to any platform.
Notes
(0000318)
rmoretti   
2013-10-25 14:06   
Taking a quick grep through the patch files, I'm guessing the issue is with the RepulsiveOnly_fa.txt and/or VirtualProteinResidue.txt patch files. They change the atom types of the HIS residue HE2 atom.

As Andy Chen notes in the his_methylated.txt patch file, there's currently no good way for patch selectors to pick out the HIS residue type without also picking out the HIS_D residue type, resulting in errors when you try to patch HIS.
(0000319)
Sergey   
2013-10-28 19:25   
Can this be reproduced with C++ Rosetta? If so, then it probably best to move it to upstream (Rosetta)





View Issue Details
296 [Rosetta] Incorrect Results minor always 2013-08-08 15:21 2014-01-09 17:55
jgray All platforms  
jadolfbr Any  
normal Any  
resolved Trunk  
open  
none    
none Trunk  
   
antibody
test/run.py -1 AntibodyInfoTest
Confirmed As Bug
56176
kink_cation_residue gives incorrect result if AbInfo is using ModifiedAHO numbering scheme
cdr_numbering_ was meant to be a set of landmark positions from which other positions can be abstracted. but it is also being used to define different stretches of loop, which makes it non-absolute.

probably need a cdr_landmarks_, and some separation of NumberingScheme idea and LoopDefinition idea
uncomment line in AntibodyInfoTest.cxxtest.cc
Select this if your bug report applies to any platform.
Notes
(0000323)
jadolfbr   
2013-12-04 14:52   
Fixed in jadolfbr/schemes. Awaiting a strange bug unrelated to changed code to push to trunk.
(0000325)
jadolfbr   
2014-01-09 17:55   
AntibodyInfo now requires a numbering scheme and a definition. Metrics can now specify which definition they are referring to, and conversion happens when using a different definition. Apps now require a numbering scheme and definition on the cmd line. http://rosettatests.graylab.jhu.edu/rev?id=56176 [^]





View Issue Details
318 [Rosetta] Crash crash always 2014-01-09 13:07 2014-01-09 14:33
rfalford12 All platforms  
Any  
normal Any  
new  
open  
none    
none  
   
Segfault in AtomTree when Setting new Fold Tree with Virtual Residues by Jump
When building a fold tree, reordering requires extracting the foldtree, reordering and then reseting this fold tree in the pose. When using the function fold_tree( FoldTree & ft_in ), even when setting an identical fold tree, the method segfaults and complains of missing residues.
Run the pilot app apps/pilot/ralford/membrane_foldtree.cc

Note that when I try to construct a fold tree, the fold tree is valid however when I try to set the same exact fold tree it crashes.
Select this if your bug report applies to any platform.
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View Issue Details
263 [Rosetta] Input Handling minor always 2013-05-01 22:37 2014-01-03 12:42
amw579 All platforms  
amw579 Any  
normal Any  
resolved  
fixed  
none    
none All  
   
Confirmed to affect oop_dock_design and hbs_dock_design; almost certain to affect homodimer_design, etc.
/scratch/amw579/rosetta/rosetta_source/bin/oop_dock_design.linuxgccrelease @flags -database /scratch/amw579/rosetta/rosetta_database/
d16b60c9d6d
ResfileReader.cc does not recognize D-canonical amino acids properly
When listing AAs other than the Big Twenty in resfile lines, you use notation like:

20 A EMPTY NC APA NC MAL NC A06

or something similar. This works fine for L and D NCAAs, whose names are their three letter codes. This does not work with D-CAAs. If you use the three letter code (i.e. DLE for D-leucine; DLY for D-lysine), ResfileReader.cc quits because those aren't in the residue type set. Looking at the line in question, it'c clear why--it's asking for the name, not the three letter code.

Unfortunately, inputting e.g.

20 A EMPTY NC DVAL NC DLYS NC DLEU

is equivalent to NATAA--it silently fails to ever design in the D amino acids. I suppose I'm not _certain_ that it's a problem with resfile parsing, but it seems likely.
Attempt to perform some kind of design with D-CAAs using a resfile.
Select this if your bug report applies to any platform.
flags (272) 2013-05-01 22:37
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=29&type=bug
Notes
(0000269)
amw579   
2013-05-02 13:30   
As far as I can tell, it looks like this would be resolved by having ResidueLevelTask::allow_noncanonical_aa to operate on the 3-letter IO_STRING of a D-CAA, since for L-CAAs, L-NCAAs, and D-NCAAs they are identical... or by making the params files for the D-CAAs have their names be the same as the 3-letter IO_STRINGs. I don't think we lose much by changing the params files in this way.
(0000270)
rmoretti   
2013-05-02 13:57   
One issue you run into is that the 3-letter IO string is not necessarily unique. There could potentially be a number of different residue types with the same 3 letter IO string. Using the full residue name allows for better control over which one you're substituting.

There's a potential to adjust the NC resfile reader to have a fall-back to using 3-letter codes if it doesn't find the the token in the full list, but you may have problems if there are multiple (potentially patched) residue types with the same 3-letter code. You'll also might run into problems where the 3-letter code contains spaces - the resfile reader might not know where that's supposed to go, as the resfile syntax ignores whitespace.

All in all, the better solution to the problem is likely better documentation that the resfile is looking for residue type names rather than three letter codes, and better awareness that they're not necessarily going to be the same. - Changing the D-CAA residue type names might address this particular issue, but sidesteps the underlying cause.
(0000271)
amw579   
2013-05-02 14:21   
In re: documentation, I don't think it's sufficient to say "please give the name, not the three letter code." Because in the status quo, _neither the name nor three letter code works_.

Giving the residue type name (i.e. DLEU) does nothing. It's equivalent to NATAA. I think when it's parsing it only grabs three characters, or something, and so it always fails a comparison to any residue names in the residue set. That's my inference; I haven't actually dug into the parser. So maybe fixing that parser would be sufficient.

Giving the three letter code fails because no residue type with that _name_ is in the residue type set.

I don't see why the 3-letter code is any more likely to contain spaces than the name, though that might be my personal misunderstanding.

Certainly, at the moment, changing the names of the 19 D-CAAs to be three characters long doesn't create name-name overlaps with anything. (After all, since all other names were identical to their 3-letter codes and all other 3-letter codes are unique, the three first letters of the D-CAAs were guaranteed to be unoccupied.)

I guess fixing the parser is the best long-term solution.
(0000274)
smlewis   
2013-05-03 17:23   
(edited on: 2013-05-03 17:24)
You did modify the residue type set to include the d-caas, right? (either residue_types.txt or -extra_res_fa?) This is in the spirit of "most likely problems first".

NC is not modifying tokens. allow_noncanonical_aa is explicitly looking for a name3.

(0000275)
smlewis   
2013-05-03 17:28   
Nevermind, I checked with my own toy problem and it duplicates, it's not -extra_res_fa
(0000276)
smlewis   
2013-05-03 17:33   
OK, so, the NC token does this:

    if ( residue_set.has_name( nc_to_include_ )){

but the packertask function does this:

            aaname == (**aas_iter).name3() )

We look for the name in the first place, and the name3 in the second. That's the bug.

I don't think it matters which way this code is unified (both to name3, or both to name), so long as it happens. I'd suggest changing NC to look for name3, not name, because otherwise I'm not sure how to get the logic in packertask to work.

Changing the dcaa's to have name3 == name will also bury the problem. (or, it did in my test).
(0000277)
smlewis   
2013-05-03 17:34   
ResidueTypeSet has has_name3, BTW. Try that first.
(0000278)
amw579   
2013-05-03 18:16   
That makes sense; I wasn't sure where to look for the conflict so it's good you were able to find it in packertask.

Yeah, it's currently working for me when I change the param files so name3 == name, too.
(0000279)
smlewis   
2013-05-03 18:19   
To be super-clear, it's in the NC token command for the resfile reader, not the packer task. If you didn't find the right line, this function of ResfileReader.cc:

void
NC::residue_action(
  PackerTask & task,
  Size resid
) const
{

  core::chemical::ResidueTypeSet const & residue_set = task.residue_task( resid ).get_original_residue_set();
  if ( residue_set.has_name( nc_to_include_ )){
    task.nonconst_residue_task(resid).allow_noncanonical_aa( nc_to_include_ );
  } else {
    std::stringstream err_msg;
    err_msg << "Unable to add non-canonical amino acid " << nc_to_include_ << " because it is not in the ResidueTypeSet for residue " << resid << ".";
    onError(err_msg.str());
  }
}//end NC

change has_name to has_name3 and give it a shot.
(0000280)
amw579   
2013-05-03 19:54   
This appears to work. Alas, I don't think I have SVN access yet (at least, it's timed out every time I've tried to log in thus far for some reason...) so I can only relate the fact that that's in fact an adequate solution on my end and maybe someone with real power can implement it.
(0000281)
smlewis   
2013-05-04 20:20   
SVN access? You know we switched the whole community to git on github last week, right? You are on rosetta-devel, right?
(0000282)
amw579   
2013-05-04 21:09   
I knew that we were going to switch to git, and I remember from minirosettacon that it was around now, but I don't think anyone ever added me to rosetta-devel, maybe for the same reason (though god knows what that is) that I never got svn access.

Oh, well. Fresh start?
(0000324)
AndrewLeaverFay   
2014-01-03 12:42   
Adding a new description for a ResidueType: its interchangeability group.

    The packer will look at all the residues types in the a given interchangeability
    group to decide which ones to allow. This functionality replaces the previous
    "name3" string which is overloaded for PDB I/O and is unnecessarily restirctive
    in length.

    The interchangeability group can be specified in the residue topology file,
    but if it is not given, then it will be set from the IO_STRING field (the name3).

    New PatchOperation classes for working with interchangeability group data.
    Moving PatchOperation class definitions from the .hh file to the .cc file.

    The "NC" ResfileOperation now uses the interchangeability group to append
    non-canonical amino acids (and other not-canonical-amino-acid residue types)
    to the ResidueLevelTask.

    Updating the interchangeability groups for the residue types defined in the
    fullatom/residue_types/rosetta_specific directory (which previously all
    shared the name3 of "XXX").

    Updating the patch files that used the SET_IO_STRING command so that they
    now also update the interchangeability group.





View Issue Details
317 [Rosetta] Crash minor always 2013-12-12 11:07 2013-12-12 11:07
rmoretti  
 
normal  
new  
open  
none    
none  
   
minirosetta
minirosetta.linuxgccrelease @flags
Growing loops can result in non-sensical loop sets and foldtrees.
If you start things right, and have the right random seed, protocols::loops::Loops::grow_all_loops( ) can result in non-sensical loop sets. Specifically, it can result in loops that grow to be ontop of one another, e.g. a loopset which has both a loop from 27-33 and a loop from 27-35. There's a little bit of detection of this case in grow_loop(nres,loop,magL,magR), but it doesn't actually change anything or prevent it from happening.

The real kicker is when the extended, overlapping loop set gets passed to something like protocols::loops::fold_tree_from_loops(), where having overlapping loops and loops with coincident start sites makes an utterly repugnant foldtree.

It might be good to have some sort of normalization/merging code for the loop growing code (or really any loop set, which may be overlapping), which would normalize and merge loops such that they meet the standard conception of a loopset.
An example which runs afoul with this using the protocols::comparative_modeling::LoopRelaxMover is posted at https://www.rosettacommons.org/node/3526 [^]

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View Issue Details
316 [PyRosetta Toolkit GUI] Bad Coding minor always 2013-12-04 14:46 2013-12-04 14:46
jadolfbr All platforms  
jadolfbr Any  
normal Any  
assigned Trunk  
open  
none    
none  
   
Confirmed As Bug
FILE->SetupPDBsForRosetta->LoadPDBLIST->select clean/analyze
CleanPDB window
Cleaning list of PDBs via PDBLIST does not work
Using the CleanPDB menu, selecting a PDBLIST to clean (change occupancies, water, hetatms, etc.) fails without any notice
Load the GUI, load a PDBLIST to clean
Select this if your bug report applies to any platform.
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View Issue Details
315 [Rosetta] Crash minor always 2013-12-04 11:04 2013-12-04 11:13
jadolfbr All platforms  
Any  
normal Any  
new Trunk  
open  
none    
none  
   
InterfaceAnalyzer
InterfaceAnalyzer.linuxclangrelease -database ../database -s 2J88_LA.pdb -no_output -tracer_data_print true
InterfaceAnalyzerMover/InterfaceAnalyzer app segfaults when waters are present
IAM should better deal with water molecules in an interface or elsewhere. At least not segfaulting, preferably identifying interface waters and giving some extra information pertaining to them.
Run IAM/InterfaceAnalyzer app with a PDB that contains water.
Confirmed for multichain and two-chain constructors
Select this if your bug report applies to any platform.
Notes
(0000322)
jadolfbr   
2013-12-04 11:13   
Note that talaris2013 scorefunction can handle waters, as can SASA calculations.





View Issue Details
11 [Rosetta] Input Handling minor always 2012-06-20 13:23 2013-11-27 07:51
rmoretti  
 
normal  
new Trunk  
open  
none    
none  
   
constraints
any
Constraints can't handle insertion codes.
While ConstraintIO::parse_residue() is able to take PDB numbering if residues are entered like "4B", where B is the chain, it does not have the ability to handle PDB numbering where the residue has an insertion code.
bcl_HTML195.html (3,600) 2013-11-27 07:51
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=39&type=bug
Notes
(0000003)
rmoretti   
2012-06-20 13:47   
c.f. http://www.rosettacommons.org/content/about-residue-number-rosetta#comment-4666 [^]
(0000005)
smlewis   
2012-06-20 15:05   
Related: I don't think the constraint documentation notes that constraints can even take PDB data at all?





View Issue Details
312 [Rosetta] Crash minor always 2013-11-19 10:17 2013-11-19 10:17
rmoretti  
 
normal  
new  
open  
none    
none  
   
CstfileToTheozymePDB
../../../main/source/bin/CstfileToTheozymePDB.linuxgccdebug -extra_res_fa rosetta_inputs/1n1.params -match:geometric_constraint_file rosetta_inputs/mocktim.cst
Confirmed As Bug
CstfileToTheozymePDB results in segmentation fault for secondary constraints.
If you pass a constraint file with a secondary constraint with less than six degrees of freedom, CstfileToTheozymePDB can segfault.

Although CstfileToTheozymePDB needs to have all six degrees of freedom specified, it should give a useful error message to that effect and gracefully exit, rather than segfaulting.
Go to Rosetta/demos/public/enzyme_design

Run

../../../main/source/bin/CstfileToTheozymePDB.linuxgccdebug -extra_res_fa rosetta_inputs/1n1.params -match:geometric_constraint_file rosetta_inputs/mocktim.cst

Note that this is the full mocktim.cst constraint file, rather than the cut down mocktim_first_2interactions_example.cst constraint file that the demo normally passes to CstfileToTheozymePDB
Thanks to Guanlin Li from the November 2013 Rosetta Workshop at Vanderbilt for finding this bug.
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View Issue Details
228 [Rosetta] Bad Coding minor always 2013-03-22 17:02 2013-11-18 16:49
rmoretti  
rmoretti  
normal  
resolved Trunk  
fixed  
none    
none  
   
many
n/a
36c2c81b7794e1f70a9520da778b3239dc3757a5
ScoreFunction cloning
Because of the distinction between ScoreFunction and SymmetricScoreFunction (as well as the other ScoreFunction subclasses), you should never use the copy constructor of ScoreFunction() to make a new copy of a ScoreFunction. Use scorefxn.clone() instead.

Note there's no drawback to this, even if you know that you have a true ScoreFunction.
To find potential violators:

egrep -R 'new[[:space:]]*ScoreFunction[[:space:]]*\([^)]' rosetta/rosetta_source/src

Command currently finds 66 instances. Some are valid, like the 7 in will and neil's apps/pilot directories, which are explicitly intended to take a symmetric scorefunction and asymmetrize it. Most of the rest are probably latent bugs.

They'll need to be checked manually, though.
Notes
(0000210)
smlewis   
2013-03-22 17:25   
Is there a future in privatizing the copy operator to force people to use clone? I am guessing not from your notes.
(0000211)
Sergey   
2013-03-22 17:28   
As Steven suggested: How about declare copy constructor and copy operator as private and never define them? That way it will be impossible to copy without clone.
(0000212)
rmoretti   
2013-03-24 19:03   
If we provide a new method for those few people who explicitly want to convert a scorefunction to the base class (with a name that makes it clear that's what they're doing), I think making the copy constructor private might work.





View Issue Details
311 [Rosetta] Input Handling minor always 2013-11-04 09:39 2013-11-05 10:53
rmoretti  
 
normal  
new  
open  
none    
none  
   
scons
scons bin mode=release extra=mpi
Bad flag in scons command doesn't give an error.
If you use "extra=mpi" instead of "extras=mpi", scons will not raise an error, but instead apparently just builds the regular version, ignoring the "extra=mpi" flag.

There probably should be some error checking on the scons input to flag this as an error.
Issue noticed by albumns on the forums https://www.rosettacommons.org/node/3483 [^]
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View Issue Details
103 [Rosetta] Input Handling minor always 2012-09-11 09:26 2013-11-05 10:53
momeara All platforms  
Any  
normal Any  
new  
open  
none    
none  
   
all
./scons.py extrass=donothing
Confirmed As Bug
scons.py doesn't reject unrecognized options
'./scons.py extra=postgres' doesn't complain, it just doesn't compile with postgres support!

also

./scons.py asdflkja=asdfasdf also doesn't complain.

run scons with an unrecognized option and watch it silently ignore it
The logic that handles this, I believe, is in tools/build/setup.py -> setup_build_options()

Select this if your bug report applies to any platform.
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View Issue Details
145 [Rosetta] Input Handling minor always 2012-10-27 15:27 2013-11-05 10:50
rpache All platforms  
weitzner Any  
normal Any  
resolved Trunk  
fixed  
none    
none Trunk  
   
loopmodel
loopmodel.linuxgccrelease -database ROSETTA_DATABASE -loops:input_pdb INPUT_PDB -loops:loop_file LOOP_FILE -loops:remodel perturb_kic -loops:refine refine_kic
bd4f744e3d3f8991df09cff9528de41e4dd04542
-loops:input_pdb is deprecated in loopmodel app after switch to JD2
Since loopmodel has been switched to JD2, the input pdb is provided using the -s flag instead of the former -loops:input_pdb. However, when one still uses the old flag, there is no warning/error message that the flag is deprecated and that -s should be used instead.

Also the documentation should be updated to reflect this change in pdb input.
run the loopmodel app, using the flag -loops:input_pdb to provide the input structure
Select this if your bug report applies to any platform.
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View Issue Details
310 [Rosetta] Crash crash always 2013-10-30 18:21 2013-10-31 08:56
amelie All platforms  
amelie Any  
normal Any  
assigned Trunk  
open  
none    
none  
   
loopmodel
loopmodel -loops:remodel perturb_kic -loops:refine refine_kic
loop modeling crashes on some input (e.g. 1ivd)
KIC crashes on 1ivd after (or while) switching to centroid but before starting any actual loop modeling. Haven't tested other protocols (like CCD).
This seems to be an issue with the HETATMs -- if stripping out all non-ATOM lines the structure is handled just fine. Somewhat surprisingly -ignore_unrecognized_res does not fix this problem. No .params files for specific ligands were supplied.
Select this if your bug report applies to any platform.
Notes
(0000320)
rmoretti   
2013-10-31 08:56   
It's probably worth noting that the HETATMs in question are for glycosylation.

Jason Labonte has been working on incorporating glycosylation loading into Rosetta - that's probably why the -ignore_unrecognized_res doesn't do anything, as the glycosylation is recognized -- in full atom mode. Likely those glycosylated residues do not yet have a centroid representation.





View Issue Details
247 [Rosetta] Bad Coding minor always 2013-04-09 10:31 2013-10-11 13:45
smlewis  
rmoretti  
normal  
resolved  
fixed  
none    
none  
   
performance benchmark (email)
N/A
30259bba8f
performance benchmark needs retuning
The performance benchmark needs retuning to have on the order of 10 seconds per test. Currently around half are under 1 second.
Here's how to do it:


It's in src/apps/benchmark/performance/ScoreEach.bench.hh. The ScoreEach instance is delcared here:

ScoreEachBenchmark Score_hpatch_("core.scoring.Score_100x_hpatch",hpatch,100);


The test activates the hpatch score term and then scores a fixed structure repeatedly. All that has to happen is that the number of repeats needs to be increased from its current value -- 100 -- to some larger one.

Notes
(0000301)
rmoretti   
2013-05-19 14:40   
I took a look at this - there's a bunch of score terms that are running insanely fast because the test protein isn't correctly set up for the score terms to do anything useful with them.

For example, there's no disulfides (so disulfide terms are very rapid), and there's no DNA/RNA, so things like dna_chi are exceedingly fast. I haven't checked all the very fast terms, but my guess is that there's some setup involved with those scoreterms which means we're not effectively profiling them, instead profiling an always-will-give-zero-energy code path.

We probably will need to add some custom protein loading to some of them to get timings that are actually meaningful.





View Issue Details
12 [Rosetta] Input Handling minor always 2012-06-20 13:46 2013-10-01 11:22
rmoretti  
olange  
normal  
assigned Trunk  
open  
none    
none  
   
constraints
any
Constraints silently eat the rest of the line.
If you naively follow the documented format of the multi-constraints like multi or ambiguous ("Constraint_Type1 Constraint_Def1 [Constraint_Type2 Constraint_Def2 [...]]"), one might put the constraints all on one line.

(As was done with rosetta_demos/public/dock_with_user_defined_constraints/rosetta_inputs/constraint_ambiguous.cst)

This is a problem as some (all?) of the constraint definitions will silently eat everything after the end of the definition to the next newline, effectively killing all but the first constraint.

It should probably be changed to either behave robustly when presented with a single line format, throw an error/warning message, or the documentation changed to make clear the sub-constraints all need to be on their own line.
c.f. http://www.rosettacommons.org/content/about-residue-number-rosetta#comment-4666 [^]
Notes
(0000004)
smlewis   
2012-06-20 15:03   
(edited on: 2012-06-20 15:04)
BOUNDED func is a function that has this "eating" behavior; it can also eat things that aren't on the line (meaning, the whole next line) if rswitch and tag are not present:

http://www.rosettacommons.org/content/maximum-number-constraints#comment-3045 [^]

(0000076)
smlewis   
2012-08-21 14:34   
GAUSSIANFUNC has the same behavior.





View Issue Details
306 [Rosetta] Bad Coding minor always 2013-09-25 13:59 2013-09-25 13:59
smlewis  
 
none  
new  
open  
none    
none  
   
git special hidden settings?
git special hidden settings?
"if this branch has already bin pushed, enable tracking with"
There's a funky spelling error in whatever code it is that generates the message on how to git-push newly made branches; it says:


"if this branch has already bin pushed, enable tracking with"
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View Issue Details
305 [Rosetta] Bad Coding minor always 2013-09-25 13:17 2013-09-25 13:51
smlewis All platforms  
Any  
low Any  
new Trunk  
open  
none    
none  
   
pose.constraint_set()
pose.constraint_set()
pose.constraint_set in NULL case
pose.constrant_set():

Pose::ConstraintSetCOP
Pose::constraint_set() const
{
    if ( constraint_set_ == 0 ) {
        return new scoring::constraints::ConstraintSet; // create an empty constraint set
    }
    return constraint_set_;
}

This has the behavior of returning a VALID pointer to an empty constraint set if the Pose has no ConstraintSet...but it doesn't set the Pose to point at that same COP! So, it returns a valid ConstraintSet that isn't actually the Pose's. Is that bad behavior?
Select this if your bug report applies to any platform.
Notes
(0000316)
smlewis   
2013-09-25 13:51   
It's because the "getter" is const, so it can't modify the
Pose::constraint_set_. The question then is, should it be nonconst?
or return NULL? or be as-is?





View Issue Details
304 [Rosetta] Crash crash sometimes 2013-09-23 15:48 2013-09-23 15:48
smlewis Mac  
OSX  
normal 10.8.5  
new Trunk  
open  
none    
none  
   
compilation error
compilation error
Confirmed As Bug
compilation error in external/boost_1_46_1/boost/mpl/aux_/preprocessed/gcc/apply.hpp [forum]
See https://www.rosettacommons.org/node/3446 [^]
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View Issue Details
53 [Rosetta] Input Handling minor unable to reproduce 2012-07-31 14:31 2013-09-16 19:33
smlewis  
dimaio  
low  
resolved  
fixed  
none    
none Trunk  
   
constraints
constraints
88623c0f028e62133994b10c3eb7ec3542e5e93d
Feature Request: MultiAmbiguousConstraint
AmbiguousConstraint takes N constraints but returns the score of the best 1. I am envisioning a class which would take N constraints but return the best M, where N <= M <= 1. This would be useful for the sort of partly-wrong constraint data Evan showed in his RosettaCON talk.
Notes
(0000040)
dimaio   
2012-07-31 14:39   
This already exists as core/scoring/constraints/KofNConstraint
(0000042)
smlewis   
2012-07-31 21:38   
I'm changing this bug to "document KofNConstraint in the constraints documentation page doc/core/scoring/constraints_file.dox"





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303 [Rosetta] Crash minor always 2013-09-13 13:02 2013-09-13 13:02
rmoretti  
 
normal  
new  
open  
none    
none  
   
rosetta_scripts
na
MutateResidue mover segfaults for terminal positions
Specifying a plain three letter residue type for the new_res option of the MutateResidue in RosettaScripts for a position that is a terminal residue results in a segfault.

See https://www.rosettacommons.org/node/3444 [^]
I'm guessing (but have not confirmed) it's an issue with patch incompatibilities. Trying to apply a plain "ALA" to a "ASP_p:CtermProteinFull" residue likely causes an error.

This sort of patch incompatibility should be detected and dealt with with an error message instead of a segfault. (Perhaps an automatic conversion of a three-letter specification to the appropriate patched type might be something to do too.)
There are no notes attached to this issue.





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302 [Rosetta] Input Handling major always 2013-09-06 15:36 2013-09-06 15:36
kimdn All platforms  
Any  
normal Any  
new Trunk  
open  
none    
none  
   
fragment_picker.linuxgccrelease
fragment_picker.linuxgccrelease @quota-protocol.flags
exclude homologues at frag_picker
@/home/kimdn/rosetta/demos/public/fragment_picker/QuotaProtocol

2jsvX.homolog_vall is defined with '2jsvX 2qmtA'

But tracer spits
"protocols.frag_picker.FragmentPicker: Excluded PDBs:

2jsvX"


While when I defined 2jsvX.homolog_vall as
'2jsvX
2qmtA'
tracer spits
"protocols.frag_picker.FragmentPicker: Excluded PDBs:

2jsvX 2qmtA 2qmt_"
which looks correct.

So I think that the homo file should be modified as the latter case.
Select this if your bug report applies to any platform.
There are no notes attached to this issue.





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301 [Rosetta] Crash crash always 2013-09-06 09:42 2013-09-06 09:45
kimdn x86  
Linux  
high Ubuntu  
new Trunk  
open  
none    
none  
   
fragment_picker
fragment_picker.linuxgccrelease @best-frags.flags
seg fault at fragment picker
With
# score name priority wght max_allowed extras
RamaScore 400 2.0 - predA
SecondarySimilarity 350 1.0 - predA
FragmentCrmsd 450 1.0 1

it dumped core.

It seems that at least 3mers are produced (while 9mers are not produced).
I attach all input/output files (crmsd_has_1_wt_and_1_max_seg_fault.zip).

I copy report at additional information.
fragment_picker.linuxgccrelease @best-frags.flags @ trunk version id 55681

http://test.rosettacommons.org/revs?revs_tgp_no=2&revs_tgp_limit=31 [^]
kimdn@contador:~/scr/run/fragment_picker/native/1ten/frag_picker/BestFragmentsProtocol/w_manually_checked_ss/crmsd_be_highest_prio_value/crmsd_has_1_wt_and_1_max$ source run_example
core.init: Rosetta version 7db9a2230de5363b620fe9f992085c8077653ab5 2013-08-26 13:00:07 -0400 from kimdn@152.19.81.197:~/rosetta/main
core.init: command: fragment_picker.linuxgccrelease @best-frags.flags
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=607751371 seed_offset=0 real_seed=607751371
core.init.random: RandomGenerator:init: Normal mode, seed=607751371 RG_type=mt19937
protocols.frag_picker.FragmentPicker: reading a query sequence from: input_files/seq_in_fasta
protocols.frag_picker.FragmentPicker: picking fragments for query sequence: LDAPSQIEVKDVTDTTALITWFKPLAEIDGIELTYGIKDVPGDRTTIDLTEDENQYSIGNLKPDTEYEVSLISRRGDMSSNPAKETFTT
protocols.frag_picker.VallProvider: vallChunksFromLibrary
protocols.frag_picker.VallProvider: Reading Vall library from /home/kimdn/rosetta/tools/fragment_tools/vall.apr24.2008.extended.gz ... startline: 1 endline: 0
protocols.frag_picker.VallProvider: ... done. Read 2330105 lines. Time elapsed: 21 seconds.
protocols.frag_picker.VallProvider: Total chunks: 13717
protocols.frag_picker.VallProvider: Largest chunk: 1264 aa
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 9172 residue types
protocols.frag_picker.FragmentPicker: Will pick fragments of size:3 9
protocols.frag_picker.FragmentPicker: Creating fragment scoring scheme
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_AP.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_S.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Q.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_V.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_K.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_V.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_A.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_W.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_F.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_KP.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_I.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Y.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_I.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_K.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_VP.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_N.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Q.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Q.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Y.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_S.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_N.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_KP.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Y.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_V.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_S.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_S.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_M.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_S.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_S.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_NP.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_A.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_K.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_F.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
protocols.frag_picker.scores.FragmentCrmsd: Reference structure to score fragments by crmsd loaded from: input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 2 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: ASP
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 6 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 8 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: GLU
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 10 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 23 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 38 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 44 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 54 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: ASN
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 55 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 60 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: ASN
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 62 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 74 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 75 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 81 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: ASN
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 84 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: LYS
core.pack.task: Packer task: initialize from command line()
protocols.frag_picker.FragmentPicker: Picking 200 fragments based on 10000 candidates
protocols.frag_picker.FragmentPicker: Creating fragment scoring scheme for the selection step
protocols.frag_picker.FragmentPicker: Collector for fragment size: 3 set to: BoundedCollector
protocols.frag_picker.FragmentPicker: Collector for fragment size: 9 set to: BoundedCollector
protocols.frag_picker.FragmentPicker: Fragment scoring scheme used:
-----------------------------------------
id fragment score method name weight
  1 FragmentCrmsd 1
  2 RamaScore 2
  3 SecondarySimilarity 1
-----------------------------------------

protocols.frag_picker.FragmentPicker:
fragment_picker: After setup; size of a query is: 89
fragment_picker: Picking candidates
fragment_picker: Running bounded protocol
protocols.frag_picker.FragmentPicker: pick fragments using bounded protocol...
protocols.frag_picker.FragmentPicker: Picking candidates...
protocols.frag_picker.FragmentPicker: 0% done at 1aoc
protocols.frag_picker.FragmentPicker: 1% done at 1baz
protocols.frag_picker.FragmentPicker: 2% done at 1c3m
protocols.frag_picker.FragmentPicker: 3% done at 1cyo
protocols.frag_picker.FragmentPicker: 4% done at 1dm5
protocols.frag_picker.FragmentPicker: 5% done at 1e8c
protocols.frag_picker.FragmentPicker: 6% done at 1eq2
protocols.frag_picker.FragmentPicker: 7% done at 1f6b
protocols.frag_picker.FragmentPicker: 8% done at 1fs0
protocols.frag_picker.FragmentPicker: 9% done at 1g7s
protocols.frag_picker.FragmentPicker: 10% done at 1gtt
protocols.frag_picker.FragmentPicker: 11% done at 1h7c
protocols.frag_picker.FragmentPicker: 12% done at 1hxs
protocols.frag_picker.FragmentPicker: 13% done at 1iir
protocols.frag_picker.FragmentPicker: 14% done at 1j2j
protocols.frag_picker.FragmentPicker: 15% done at 1jh6
protocols.frag_picker.FragmentPicker: 16% done at 1jwi
protocols.frag_picker.FragmentPicker: 17% done at 1kcg
protocols.frag_picker.FragmentPicker: 18% done at 1kxo
protocols.frag_picker.FragmentPicker: 19% done at 1ll2
protocols.frag_picker.FragmentPicker: 20% done at 1m40
protocols.frag_picker.FragmentPicker: 21% done at 1ml9
protocols.frag_picker.FragmentPicker: 22% done at 1n4x
protocols.frag_picker.FragmentPicker: 23% done at 1nkr
protocols.frag_picker.FragmentPicker: 24% done at 1nyk
protocols.frag_picker.FragmentPicker: 25% done at 1ocs
protocols.frag_picker.FragmentPicker: 26% done at 1orf
protocols.frag_picker.FragmentPicker: 27% done at 1p9r
protocols.frag_picker.FragmentPicker: 28% done at 1psq
protocols.frag_picker.FragmentPicker: 29% done at 1q7s
protocols.frag_picker.FragmentPicker: 30% done at 1qop
protocols.frag_picker.FragmentPicker: 31% done at 1r5m
protocols.frag_picker.FragmentPicker: 32% done at 1rp3
protocols.frag_picker.FragmentPicker: 33% done at 1s3z
protocols.frag_picker.FragmentPicker: 34% done at 1six
protocols.frag_picker.FragmentPicker: 35% done at 1t0h
protocols.frag_picker.FragmentPicker: 36% done at 1tdh
protocols.frag_picker.FragmentPicker: 37% done at 1tuv
protocols.frag_picker.FragmentPicker: 38% done at 1u6l
protocols.frag_picker.FragmentPicker: 39% done at 1uli
protocols.frag_picker.FragmentPicker: 40% done at 1uxo
protocols.frag_picker.FragmentPicker: 41% done at 1v9m
protocols.frag_picker.FragmentPicker: 42% done at 1vim
protocols.frag_picker.FragmentPicker: 43% done at 1vpv
protocols.frag_picker.FragmentPicker: 44% done at 1w2w
protocols.frag_picker.FragmentPicker: 45% done at 1wfx
protocols.frag_picker.FragmentPicker: 46% done at 1wui
protocols.frag_picker.FragmentPicker: 47% done at 1x8h
protocols.frag_picker.FragmentPicker: 48% done at 1xkp
protocols.frag_picker.FragmentPicker: 49% done at 1xxg
protocols.frag_picker.FragmentPicker: 50% done at 1yar
protocols.frag_picker.FragmentPicker: 51% done at 1ym3
protocols.frag_picker.FragmentPicker: 52% done at 1yz7
protocols.frag_picker.FragmentPicker: 53% done at 1zd1
protocols.frag_picker.FragmentPicker: 54% done at 1zud
protocols.frag_picker.FragmentPicker: 55% done at 2a5y
protocols.frag_picker.FragmentPicker: 56% done at 2aja
protocols.frag_picker.FragmentPicker: 57% done at 2aze
protocols.frag_picker.FragmentPicker: 58% done at 2bay
protocols.frag_picker.FragmentPicker: 59% done at 2bmb
protocols.frag_picker.FragmentPicker: 60% done at 2c1x
protocols.frag_picker.FragmentPicker: 61% done at 2cgh
protocols.frag_picker.FragmentPicker: 62% done at 2cx1
protocols.frag_picker.FragmentPicker: 63% done at 2dbb
protocols.frag_picker.FragmentPicker: 64% done at 2dqw
protocols.frag_picker.FragmentPicker: 65% done at 2e4u
protocols.frag_picker.FragmentPicker: 66% done at 2et1
protocols.frag_picker.FragmentPicker: 67% done at 2f6h
protocols.frag_picker.FragmentPicker: 68% done at 2fh5
protocols.frag_picker.FragmentPicker: 69% done at 2fsu
protocols.frag_picker.FragmentPicker: 70% done at 2g5g
protocols.frag_picker.FragmentPicker: 71% done at 2gia
protocols.frag_picker.FragmentPicker: 72% done at 2gtr
protocols.frag_picker.FragmentPicker: 73% done at 2h5e
protocols.frag_picker.FragmentPicker: 74% done at 2hev
protocols.frag_picker.FragmentPicker: 75% done at 2hqt
protocols.frag_picker.FragmentPicker: 76% done at 2i3t
protocols.frag_picker.FragmentPicker: 77% done at 2ics
protocols.frag_picker.FragmentPicker: 78% done at 2inp
protocols.frag_picker.FragmentPicker: 79% done at 2j01
protocols.frag_picker.FragmentPicker: 80% done at 2jae
protocols.frag_picker.FragmentPicker: 81% done at 2nnr
protocols.frag_picker.FragmentPicker: 82% done at 2nwh
protocols.frag_picker.FragmentPicker: 83% done at 2o3i
protocols.frag_picker.FragmentPicker: 84% done at 2obw
protocols.frag_picker.FragmentPicker: 85% done at 2ols
protocols.frag_picker.FragmentPicker: 86% done at 2oyc
protocols.frag_picker.FragmentPicker: 87% done at 2p6r
protocols.frag_picker.FragmentPicker: 88% done at 2ph3
protocols.frag_picker.FragmentPicker: 89% done at 2pu9
protocols.frag_picker.FragmentPicker: 90% done at 2q4e
protocols.frag_picker.FragmentPicker: 91% done at 2qg7
protocols.frag_picker.FragmentPicker: 92% done at 2qqh
protocols.frag_picker.FragmentPicker: 93% done at 2qzb
protocols.frag_picker.FragmentPicker: 94% done at 2rio
protocols.frag_picker.FragmentPicker: 95% done at 2v1x
protocols.frag_picker.FragmentPicker: 96% done at 2yxb
protocols.frag_picker.FragmentPicker: 97% done at 3b57
protocols.frag_picker.FragmentPicker: 98% done at 3bja
protocols.frag_picker.FragmentPicker: 99% done at 5nul
protocols.frag_picker.FragmentPicker: ... done. Processed 13717 chunks. Time elapsed: 2659 seconds.
protocols.frag_picker.FragmentPicker: Saving Fragments...
Segmentation fault (core dumped)
crmsd_has_1_wt_and_1_max_seg_fault.zip (1,071,098) 2013-09-06 09:42
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=38&type=bug
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View Issue Details
282 [Rosetta] Bad Coding minor always 2013-06-12 13:30 2013-08-29 13:43
rmoretti  
 
normal  
new  
open  
none    
none  
   
demos/public/dock_ligand_and_proteins/scripts/clean_pdb.py
python clean_pdb.py
Python imports issues
Some Rosetta scripts (such as demos/public/dock_ligand_and_proteins/scripts/clean_pdb.py) rely on other python modules (like source/src/python/apps/public/amino_acids.py), but when copied or run in different directories, those modules might not be on the Python path for other users.

Some common location & path should be made for these sorts of resources.
See also https://www.rosettacommons.org/node/3317 [^]
Notes
(0000314)
rmoretti   
2013-08-29 13:43   
Another option is to do sys.path manipulation at the top of scripts files to autodiscover the path to the module directories





View Issue Details
294 [Rosetta] Crash minor always 2013-07-25 10:22 2013-08-17 13:39
khouli All platforms  
sarel Any  
normal Any  
assigned  
open  
none    
none  
   
rosetta_scripts
rosetta_scripts.mpipostgres.macosgccrelease
AtomTree mover in rosetta scripts seg faults for residues with less than 4 atoms
The AtomTree mover in rosetta scripts crashes on residues with < 4 residues like metals or water.
Input is a pdb containing a protein and also residues with less than 4 atoms in their param file (ex: metal ions, water).

Running a rosetta script that only applies the AtomTree mover results in a seg fault.

I've tried this with MG and TP3 water with the simple_ft and docking_ft options.
The seg fault happens in Conformation::get_torsion_angle_atom_ids() when the residue is unable to return four atoms to define a "mainchain" torsion
Select this if your bug report applies to any platform.
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299 [Rosetta] Incorrect Results minor always 2013-08-12 13:10 2013-08-12 13:10
khouli All platforms  
Any  
normal Any  
new  
open  
none    
none  
   
na
na
Registering NeighborsByDistanceCalculator with same name as a removed calc creates bad neighbor entries
Registering a NeighborsByDistanceCalculator, using it, removing it, then register one with the same name. The new one has the neighbor values of the old one and doesn't recognize the need to update.

CalculatorFactory::Instance().register_calculator("myCalc", new NeighborsByDistanceCalculator(some_res) );

// run calc, fill vector of neighbors, do stuff...

CalculatorFactory::Instance().remove_calculator("myCalc");
CalculatorFactory::Instance().register_calculator("myCalc", new NeighborsByDistanceCalculator(other_res) );

// calculator now mapped to "myCalc" has neighbor entries from first calc mapped to "myCalc"
With a function called repeatedly in a loop that does the steps:

CalculatorFactory::Instance().register_calculator("myCalc", new NeighborsByDistanceCalculator(some_res) );
CalculatorFactory::Instance().remove_calculator("myCalc");
CalculatorFactory::Instance().register_calculator("myCalc", new NeighborsByDistanceCalculator(other_res) );

All calculators return the same vector of neighbors even for distant residues.
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View Issue Details
298 [Rosetta] Input Handling minor always 2013-08-12 09:51 2013-08-12 09:51
AndrewLeaverFay All platforms  
sarel Any  
normal Any  
assigned Trunk  
open  
none    
none  
   
rosetta_scripts
/path/to/rosetta_scripts.default.linuxgccrelease -database /path/to/Rosetta/main/database -s 1ubq.pb -ignore_unrecognized_res -parser:script repack.xml
Confirmed As Bug
Name collision doesn't produce an error message
If you create a score function in the SCOREFXNS blaock and give it the same name as one of the default score functions, rosetta_scripts will simply ignore your score function and use the existing one. Instead, it should either exit with an error message listing the names of all the score functions that cannot / should not be overwritten, OR it should overwrite the default score function.
call this repack.xml
<ROSETTASCRIPTS>
  <SCOREFXNS>
    <talaris2013 weights="talaris2013.wts">
      <Reweight scoretype=pro_close weight=0.0 />
      <Reweight scoretype=cart_bonded weight=0.5 />
    </talaris2013>
  </SCOREFXNS>
  <TASKOPERATIONS>
    <RestrictToRepacking name=repack />
  </TASKOPERATIONS>
  <MOVERS>
    <PackRotamersMover name=repack task_operations=repack scorefxn=talaris2013>
  </MOVERS>
   <OUTPUT scorefxn=talaris2013/>
</ROSETTASCRIPTS>
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280 [Rosetta] Bad Coding minor always 2013-06-05 20:47 2013-07-25 17:30
delucasl All platforms  
jadolfbr Any  
normal Any  
assigned Trunk  
open  
none    
none  
   
All
Anything that computes an hbond
Confirmed As Bug
HbondSet::HbondSet(pose) only computes bb-bb bonds
HbondSet::HbondSet(pose) calls setup_for_residue_pair_energies() with the backbone_only flag set to true. This is a fairly counterintuitive default behavior, and the switch should probably be flipped, assuming existing code isn't relying on the current behavior
Select this if your bug report applies to any platform.
Notes
(0000302)
jadolfbr   
2013-06-05 21:08   
I have a fix for this in jadolfbr/hbond_interface. I'll be committing it soon.
(0000308)
jadolfbr   
2013-07-25 11:12   
(edited on: 2013-07-25 11:20)
I added an option to the pose constructor for bb_only boolean, with the default true to trunk (https://github.com/RosettaCommons/main/commit/1df8171ffc09b0d9abf4595747421ea0c23f74fb [^]) . I also updated the code documentation. To flip the switch on the default, I would need to find the pose constructor throughout code - How can this be done reliably?

(0000309)
rmoretti   
2013-07-25 17:30   
Probably the easiest way of finding all the places where a particular C++ function is called in the code is to change the interface of the function, and look for all the places the compiler complains.

For your purposes, just remove the default option on the HBondSet constructor, recompile, (temporarily) fix all the places where it complains about the missing constructor to be explicit about the parameter, and keep repeating until the code compiles without issue. You'll then have identified all the location where that function has been called. (Or at least those locations which are actively being compiled.)





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293 [Rosetta] Bad Coding minor always 2013-07-24 17:52 2013-07-24 17:52
amelie All platforms  
Any  
normal Any  
new All  
open  
none    
none  
   
ddg_monomer
ddg_monomer -ddg::local_opt_only -ddg::output_silent false -ddg::dump_pdbs true
ddG with local optimization enforces silent files
When running the ddg_monomer application with the local repacking option (-ddg::local_opt_only) it isn't possible to generate PDB files, even when providing -ddg::output_silent false -ddg::dump_pdbs true.
ddg_monomer -ddg::local_opt_only -ddg::output_silent false -ddg::dump_pdbs true

(will produce a silent file, not PDBs)
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View Issue Details
292 [Rosetta] Crash minor always 2013-07-19 22:07 2013-07-22 19:41
rmoretti  
delucasl  
normal  
resolved  
fixed  
none    
none  
   
rosetta_scripts
na
Confirmed As Bug
06b47ca
Missing chains cause segfault in LigandDocking
Using the Translate or Rotate movers with a chain= designation which does not exist in the pose results in a segmentation fault.

In debug mode it throws an assertion error (during the parse_my_tags phase)

core::Size core::pose::get_chain_id_from_chain(const char&, const core::pose::Pose&): Assertion `chain_ids.size() == 1' failed.

A more helpful error message should be presented to the user.
cf. forum post https://www.rosettacommons.org/node/3381 [^]
Notes
(0000307)
delucasl   
2013-07-22 19:41   
Fixed, core::pose::get_chain_id_from_chain throws an EXCN_RangeError with message chain_id X does not exist





View Issue Details
291 [Rosetta] Bad Coding major always 2013-07-19 10:58 2013-07-19 14:04
AndrewLeaverFay All platforms  
AndrewLeaverFay Any  
urgent Any  
resolved Trunk  
fixed  
none    
none Trunk  
   
all
-nblist_autoupdate
Confirmed As Bug
e5a8135
FA_Elec / HackElec derivatives wrong when using nblist_autoupdate
The derivatives for hack-elec are not evaluated when using nblist_autoupdate. They haven't been evaluated since r38314 (https://svn.rosettacommons.org/trac/changeset/38314/trunk/mini/src/core/scoring/hackelec/HackElecEnergy.cc [^]). They are just fine if you're not using nblist_autoupdate, however.

This surely effects any protocol that uses nblist_autoupdate and the new default score function, Talaris2013.
Select this if your bug report applies to any platform.
Notes
(0000306)
AndrewLeaverFay   
2013-07-19 14:04   
Reinstated code commented out in r38314 and deleted in r47618. Added unit tests to make sure that derivative evaluation with the use_nblist_autoupdate flag works properly (and won't get broken carelessly again).

Thanks, Frank, for finding this bug!





View Issue Details
290 [Rosetta] Incorrect Results major always 2013-07-09 17:06 2013-07-15 10:26
momeara All platforms  
AndrewLeaverFay Any  
normal Any  
resolved Trunk  
fixed  
none    
none Trunk  
   
rosetta_scripts FastRelax standard mover
standard rosetta_scripts command line
Confirmed As Bug
55496
Loss of Density in Heavy Atom Distances of 2.855A
There seems to be a loss of density at heavy atom distances of 2.855A (At least HBonding heavy atom Acceptor - Donor distances). It seems to be caused by one of these flags:
    -corrections::chemical:icoor_05_2009
    -analytic_etable_evaluation
    -use_bicubic_interpolation
    -dun10
    -set_atom_properties fa_standard:ONH2:LK_DGFREE:-5.85 fa_standard:NH2O:LK_DGFREE:-7.8 fa_standard:Narg:LK_DGFREE:-10.0 fa_standard:OH:LK_DGFREE:-6.70

It is apparent in bb->bb and sc->sc hbonds so my guess is that it is caused by a concave derivative discontinuity in the analytic_etable evaluation code.


Evidence: for plots, see attached tar.gz

  
For Talaris2013 (trunk) energy function, For Asp/Glu -> Lys hbonds:
     top8000 relaxed natives with no energy function flags
     O->N distance distribution with a tight kernel shows a striking loss of density at 2.855A
          Talaris2013_CXL_AMO_hbond_ADdist_130709.pdf
     O->N vs O->H scatter plot, shows the loss is correlated with the O->N distance
          hbond_geo_dim_pairs_scatter_ADdist_AHdist_chem_type_Talaris2013_130709.pdf

Score12 energy function, backbone->backbone hbonds:
      top8000 relaxed natives with flags:
           -restore_pre_talaris_2013_behavior
      O->N distance distribution with tight kernel zoomed in shows no loss of density at 2.855A
           hbond_ADdist_bb_bb_zoom_Score12_130709.pdf

Baseline energy function, backbone->backbone hbonds:
      top8000 relaxed natives with flags:
          -restore_pre_talaris_2013_behavior
          -corrections::chemical:icoor_05_2009
          -analytic_etable_evaluation
          -use_bicubic_interpolation
          -dun10
          -set_atom_properties fa_standard:ONH2:LK_DGFREE:-5.85 fa_standard:NH2O:LK_DGFREE:-7.8 fa_standard:Narg:LK_DGFREE:-10.0 fa_standard:OH:LK_DGFREE:-6.70
            <s weights=score12prime>
                <Reweight scoretype=fa_sol weight=0.75/>
                                                                                                                                                                                                                
                This was mistakenly set to 0.575 which is not .5 * 1.17
                <Reweight scoretype=hbond_sr_bb weight=0.585/>
                                                                                                                                                                                                                
                Enable the new disf
                <Reweight scoretype=dslf_ss_dst weight=0/>
                <Reweight scoretype=dslf_cs_ang weight=0/>
                <Reweight scoretype=dslf_ss_dih weight=0/>
                <Reweight scoretype=dslf_ca_dih weight=0/>
                <Reweight scoretype=dslf_fa13 weight=1.0/>
        </s>
      O->N distance distribution with tight kernel zoomed in shows loss of density at 2.855A
           hbond_ADdist_bb_bb_zoom_Baseline_130709.pdf
       
I see the problem in relax natives
Select this if your bug report applies to any platform.
long_dip.zip (231,129) 2013-07-09 17:06
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=37&type=bug
Notes
(0000305)
AndrewLeaverFay   
2013-07-15 10:26   
https://github.com/RosettaCommons/main/compare/5e4b5398ab...234478ca15 [^]





View Issue Details
287 [Rosetta] Crash minor always 2013-06-26 15:32 2013-07-10 18:55
rmoretti  
rmoretti  
normal  
resolved Trunk  
fixed  
none    
none  
   
score_jd2, but likely any.
score_jd2.linuxgccrelease -s NCmodification.pdb -out:pdb -overwrite -in:Ntermini B -in:Ctermini A
a9caa5d244fd677aabcdb6d63252236131e522b2
Consecutive modified termini result in errors.
Attempting to load/score a pose with chain 1 being c-terminally modified with C-methylamidation and chain 2 N-terminally modified with acetylation results in a free(): invalid pointer error.
Run:

score_jd2.linuxgccrelease -s NCmodification.pdb -out:pdb -overwrite -in:Ntermini B -in:Ctermini A

Doing the same with NCmodification_flip.pdb, which is the same but simply with the A and B chains flipped in order (but not renamed) does not result in this error.
NCmodification.pdb (7,928) 2013-06-26 15:32
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=35&type=bug
NCmodification_flip.pdb (7,928) 2013-06-26 15:32
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=36&type=bug
Notes
(0000304)
rmoretti   
2013-07-10 18:55   
Bug was caused by (erroneously) attempting to chemically connect the two termini.





View Issue Details
289 [Rosetta] Crash minor always 2013-07-02 14:32 2013-07-02 14:32
kdrew All platforms  
Any  
normal Any  
new All  
open  
none    
none  
   
all
./bin/fixbb.linuxgccrelease -help
crash after printing out help

When running any(?) app with the single argument of '-help' an uncaught exception crashes the program.

-snip-
...
stochastic_pack | false | B| Pack using a continuous
                               | | | sidechains rotamer library

terminate called after throwing an instance of 'std::string'
Aborted
-snip-

There are two issues.

1. The 'std_exit_wrapper' function in utility/options/OptionCollection.cc throws an illegal exception of type std::string. This should not be allowed and should throw an excn::EXCN_Msg_Exception.

2. If 'std_exit_wrapper' is called with EXIT_SUCCESS, it should not throw an exception at all. This is what is happening after the help message is printed.

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285 [Rosetta] Incorrect Results minor always 2013-06-25 17:12 2013-07-02 14:01
delucasl All platforms  
delucasl Any  
normal Any  
resolved  
fixed  
none    
none Trunk  
   
any time membrane scoring is involved
any
Confirmed As Bug
736e60e
MembraneTopology uses an assert to test size of allow_scoring_
allow_scoring() relies on an assert to make sure allow_scoring is the right size of this, but the size of this is set manually in the spanfile. Thus, the error check is not caught in release mode
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288 [Rosetta] Input Handling minor always 2013-06-26 15:49 2013-06-26 15:49
rmoretti  
 
normal  
new  
open  
none    
none  
   
all
any
Feature Request
Rosetta doesn't automatically recognize chain terminal modifications.
If you load a PDB with modified (N-acetylated, C-methamidated, etc.) chain termini, Rosetta will ignore the atoms for that modificationby default. You need to explicitly add the flags -in:Ntermini and -in:Ctermini explicitly listing the chains for which you wish to load the modified chain termini for.

Ideally Rosetta should be able to automatically recognize that there is a (properly named) acetyl/etc group on that residue, and load the appropriate patched residue type for that residue.
The reason the patched residue isn't loaded is that there is a check for UPPER_TERMINUS and LOWER_TERMINUS variant types for those residues which start/end chains.

Adding the TERMINUS variant types to the chain terminating patches might be a solution, but there appears to be some issues with properly creating the foldtree in those situations.
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View Issue Details
286 [Rosetta] Crash minor always 2013-06-25 18:26 2013-06-25 18:26
jgray All platforms  
Any  
normal Any  
new Trunk  
open  
none    
none  
   
any that use constraints, centroid/fullatom, and KIC
antibody-
Constraints crash if fullatom and centroid mode and KIC are mixed
One can load constraints to a fullatom pose, then switch to centroid, then model a loop without using any constraints, the program crashes.
run the antibody_H3 integration test at commit ccd99871a656824d4ec1b422336ab6270809f74b (June 19, 2013) with the cst_fa file from commit 050d24467d456fe44ac2ed75392cc01298aa82c1. In the latter commit, a workaround was put into the antibody code.
Best solution would be to stash fullatom and centroid constraints in separate places in pose.

Next solution is to have an assert in the loop-residue-mapping routines that ignore constraints if they are for a residue-type-set that is not current

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284 [Rosetta] Input Handling minor always 2013-06-19 10:12 2013-06-19 10:12
ralford All platforms  
Any  
normal Any  
new Trunk  
open  
none    
none  
   
dockingprotocol
See steps to reproduce***
Confirmed As Bug
Docking Protocol Segfaults when Passed Symmetry Flags
in the user documentation, it is defined that the Docking protocol does not support symmetry (symmetry definition files, etc) and to use the symmetric docking protocol instead. However, if in error, symmetry options are passed to Docking, Docking will throw an error and segfault. Docking should just throw an error and not crash in that way.
PDB: 1afo.pdb (Glycophorin A)

Run Command: docking_protocol.macosgccrelease -database /path/to/db @flags

Contents of Flags File:
# Input Option Group
-s 1afoA_relaxed.pdb
-run:constant_seed
-out:nstruct 1
#
# Docking Options
-docking:partners A_B
-dock_pert 3 8
-run:max_retry_job 10
-docking:sc_min
-packing:ex1
-packing:ex2aro
#
# Symmetry Options
-symmetry:symmetry_definition ../1afo.c2.symm
-symmetry:initialize_rigid_body_dofs
-symmetry:symmetric_rmsd
#
# Add scoring options
-evaluation:gdtmm
-evaluation:rmsd
-overwrite
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283 [Rosetta] Crash major always 2013-06-17 05:58 2013-06-17 14:29
jwillis0720 X86  
delucasl Linux  
high CentOS  
assigned Trunk  
open  
none    
none  
   
rosetta_scripts
rosetta_scripts.mpimysql and rosetta_scripts.mysql
Confirmed As Bug
New database schema fails for mysql features reporters
Fails on bad foreign key constraint whenever trying to use mysql database features reporter.

So far I have found that it fails for scores and residue type features reporters:
 
<feature name=ScoreTypeFeatures/>
 <feature name=ResidueFeatures/>
 <feature name=ResidueTotalScoresFeatures scorefxn=score12/>
 <feature name=ResidueScoresFeatures scorefxn=score12/>
   
Getting this error:
ERROR: cppdb::mysql::Cannot add or update a child row: a foreign key constraint fails (`production_run_no_tys`.`batch_reports`, CONSTRAINT `batch_reports_ibfk_2` FOREIGN KEY (`report_name`) REFERENCES `features_reporters` (`report_name`))
ERROR:: Exit from: src/basic/database/sql_utils.cc line: 553
Must have mysql server running:

Then a short xml:
<dock_design>
    <SCOREFXNS>
    </SCOREFXNS>
    <FILTERS>
        </FILTERS>
    <TASKOPERATIONS>
    </TASKOPERATIONS>
        <MOVERS>
        <ReportToDB name=features database_mode=mysql database_name="production_run_no_tys" batch_description="primary">
        <feature name=ScoreTypeFeatures/>
        <feature name=ResidueFeatures/>
        <feature name=ResidueTotalScoresFeatures scorefxn=score12/>
         <feature name=ResidueScoresFeatures scorefxn=score12/>
        <feature name=StructureScoresFeatures scorefxn=score12/>
    </ReportToDB>
    </MOVERS>
        <APPLY_TO_POSE>
        </APPLY_TO_POSE>
        <PROTOCOLS>
            <Add mover_name=features/>
        </PROTOCOLS>
</dock_design>


and a flags file:
-parser
    -protocol scoring_to_db.xml
-database path/to/db
-inout:dbms
    -mode mysql
    -host vacseq.mc.vanderbilt.edu
    -user root
    -port 37201
    -password ******
    -database_name production_run_no_tys
-out
    -use_database
-jd2
    -delete_old_poses

Any protein will work.
I have checked this pre_talaris, and post talaris. It is found after the major database scheme changes.

Bug is found in both mpi and regular build.
Notes
(0000303)
delucasl   
2013-06-17 14:28   
If you remove these 3 lines:

<feature name=ResidueTotalScoresFeatures scorefxn=score12/>
<feature name=ResidueScoresFeatures scorefxn=score12/>
<feature name=StructureScoresFeatures scorefxn=score12/>

From the XML, it works, so its definitely a problem with one of those. I'm swamped right now i'll look, at this again in a few days





View Issue Details
281 [Rosetta] Crash minor always 2013-06-10 19:50 2013-06-11 13:34
rmoretti  
rmoretti  
normal  
resolved  
fixed  
none    
none  
   
docking_protocol
docking_protocol.linuxgccrelease -s 1brs.pdb -ex1 -ex2aro -use_input_sc -no_filters -docking_local_refine -dock_min -out:pdb
Confirmed As Bug
9456691412c6900df7e71dda50518aa0c1e7cf30
DockMinMover doesn't appropriately initialize MonteCarlo Object
If you run certain structures through fullatom minimization refinement docking, they can error out with a total_residue() != 0 assertion error.

From debugging, it looks to be because the first run of the TrialMover fails, leading to the MonteCarlo object resetting the pose to the last_accepted_ pose, which can be an empty pose because mc_ wasn't appropriately initialized.

I believe that uncommenting source/src/protocols/docking/DockMinMover.cc line 142 should fix the issue, although this results in a number of integration test changes on the server. (Reasonable or not, I don't know.)

Hat tip to albumns and tfliu on the forums for finding this issue. https://www.rosettacommons.org/content/protein-docking-failed [^]
1brs.pdb (269,706) 2013-06-10 19:50
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=34&type=bug
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View Issue Details
279 [Rosetta] Crash minor always 2013-05-31 13:25 2013-05-31 13:25
rmoretti  
 
normal  
new  
open  
none    
none  
   
rosetta_scripts, rosettaDNA
rosettaDNA.linuxgccrelease @design.flags
RestrictDesignToProteinDNAInterface lacks error checking
If you give RestrictDesignToProteinDNAInterface a dna_defs string that contains a position that doesn't occur in the pose, you'll get a segmentation fault.
Go to demos/protocol_capture/2010/RosettaScripts/RosettaDNA.

Edit design.script to change the dna_defs string to a position that doesn't occur in the pose.

Run the demo.
Hat tip to Brett on the forums for finding this: https://www.rosettacommons.org/node/3305#comment-6274 [^]
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277 [Rosetta] Bad Coding minor always 2013-05-22 15:14 2013-05-22 18:29
kylebarlow  
kylebarlow  
low  
resolved Trunk  
open  
none    
none  
   
cmake
cmake
55248
CMake policy CMP0011 not set
CMake versions newer than 2.8.10.1 give a warning if policy CMP0011. Running "cmake --help-policy CMP0011" gives relevant info.
Run "cmake ." in main/source/cmake/build_release after running "./build_projects.py all"
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View Issue Details
276 [Rosetta] Crash minor always 2013-05-22 12:26 2013-05-22 12:26
rmoretti  
 
normal  
new  
open  
none    
none  
   
rosetta_scripts
rosetta_scripts -parser:protocol dockdesigndock.xml
DockingProtocol does not correctly reset input pose on sequence changes
If you call the protocols::docking::DockingProtocol mover with the low resolution stage twice, with a modification to the sequence in between, the ReturnSidechainMover in the centroid->fullatom transition will error out, as the cached input_pose_ will have a different sequence from the now mutated pose.
Something like the following (untested) XML file should trigger it

<ROSETTASCRIPTS>
   <MOVERS>
        <DockingProtocol name=dock docking_local_refine=0 dock_min=0 partners="A_B" />
        <PackRotamersMover name=redesign />
    </MOVERS>
    <PROTOCOLS>
        <Add mover=dock/>
        <Add mover=redesign/>
        <Add mover=dock/> -- Will complain about the changed sequence
    </PROTOCOLS>
</ROSETTASCRIPTS>
Thanks to Jarod from the RosettaCommons forum for finding this: https://www.rosettacommons.org/node/3290#comment-6229 [^]
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View Issue Details
275 [Rosetta] Bad Coding minor always 2013-05-21 13:41 2013-05-21 13:41
rmoretti  
 
normal  
new  
open  
none    
none  
   
rosetta_scripts
na
BackrubDD doesn't handle non-dimers very well.
BackrubDD has options to control partner1/partner2 backrubbing, but this only works for the two chain complex. If there are more than two chains (e.g. a dimer of dimers) you don't have the same control as a two-chain dimer.
Report from Jarod on the RosettaCommons forum: https://www.rosettacommons.org/node/3291#comment-6217 [^]
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29 [Rosetta] Crash crash unable to reproduce 2012-06-26 13:17 2013-05-21 09:51
smlewis  
ronj  
low  
resolved  
fixed  
none    
none  
   
pmut_scan_parallel, ??
??
53570
"Problem in calculating overlap between atoms. Termination calculation."
(from the boards, http://www.rosettacommons.org/content/problem-calculating-overlap-between-atoms-error-occurred-point-mutant-scan-application [^])

Hi all,
I'm trying to run pmut_scan_parallel application with "-score:weights design_hpatch.wts" scoring function, as suggested in manual. However, it always exits from: src/core/scoring/sasa.cc line 215 and an error reported:
"Problem in calculating overlap between atoms. Termination calculation.
radius_a: 3.16, radius_b: 3.16, distance_ijxyz: 14.199, cosine theta: 2.245"
Does it mean that atom a and b are too far from each other so that there is no overlap between them? Why it happens in hpatch scoring, and any suggestion to avoid it?
Many thanks,
xfliu
Ron says he knows how to fix it and will when he gets a chance
Notes
(0000139)
ronj   
2013-02-05 17:26   
Problem was with re-initialization of certain variables in the HPatchIG when multiple packing cycles (ndruns, not common) or the MultiCoolAnnealer are in use. Rosetta indicates the bug occurs when it's calculating atom-atom overlaps for SASA determination, even though it has nothing to do with that. Fixed by re-initing the right vectors in the HPatchIG after each annealing run.
(0000142)
smlewis   
2013-02-24 20:38   
change closed -> resolved (was fixed, not a nonbug)





View Issue Details
274 [Rosetta] Crash minor always 2013-05-20 13:43 2013-05-20 13:43
rmoretti  
 
normal  
new  
open  
none    
none  
   
rosetta_scripts
XMLs with any DesignRepackMover and minimize_rb options
DesignRepackMover doesn't handle parsed minimize_rb correctly.
In the parse_my_tag function of DesignRepackMover, if the minimize_rb option is set, it attempts to pass a single bool to min_rb(), which is expecting a vector of bools, one for each jump. Subsequent use results in an error because the vector isn't of the correct length.
hat tip to jarod for finding this https://www.rosettacommons.org/node/3291 [^]

The logic here is a bit flakey to begin with, as the number of jumps at parse time isn't necessarily going to be the number of jumps at apply time.
There are no notes attached to this issue.





View Issue Details
272 [Rosetta] Incorrect Results major always 2013-05-13 16:23 2013-05-13 16:23
delucasl All platforms  
Any  
normal Any  
new Trunk  
open  
none    
none  
   
all
all
Potentially incorrect logic in protocols::motifs::add_motif_sc_constraints
protocols::motifs::add_motif_sc_constraints makes constraints involving a current residue and the first protein residue.Usually the residue is a protein residue, but if it's not, the variable first_protein_resi is set to have the value of the first protein residue. The problem is that this value is not properly used when constructing the constraint. In other words, this code:

    cst_set->add_constraint(
        new CoordinateConstraint(
            core::id::AtomID( index2, this_pos ),
            core::id::AtomID( pose.residue( first_protein_resi ).atom_index( "CA" ), 1 ),
            inv_rotamer.xyz( index2 ),
            new HarmonicFunc( 0.0, 1.0 ) ) );

should instead read

    cst_set->add_constraint(
        new CoordinateConstraint(
            core::id::AtomID( index2, this_pos ),
            core::id::AtomID( pose.residue( first_protein_resi ).atom_index( "CA" ), first_protein_resi ),
            inv_rotamer.xyz( index2 ),
            new HarmonicFunc( 0.0, 1.0 ) ) );


Is this correct? I found this while refactoring and it's in code i'm not familiar with.
Select this if your bug report applies to any platform.
There are no notes attached to this issue.





View Issue Details
34 [Rosetta] Incorrect Results major unable to reproduce 2012-07-02 15:19 2013-05-13 11:31
smlewis  
jwillis0720  
normal  
assigned  
open  
none    
none  
   
all that use resfiles (fixbb promeniently)
fixbb -resfile resfile_that_mutates -s pdb_with_pre-existing_postransmod.pdb
Packer won't mutate a post-trans-mod residue
This is ported from an email report from Jordan Willis:

Hi,

I was wondering if anyone is aware that the resfile command:

NUM CHAIN PIKAA <canonical AA>

will not replace the AA if the AA you are going to replace, has a post translational modification. I have only discovered this on a PDB that originally contained sulfated tyrosines when I tried to mutate those tyrosines to a canonical AA.

Is this a known issue? Or is it an issue?

Jordan
(as yet unconfirmed)
Notes
(0000082)
smlewis   
2012-08-22 16:24   
not assigned: returning to red angry
(0000294)
smlewis   
2013-05-13 11:31   
Some notes from the email thread about this:

the problem here is in variant matching.

In this function:
void ResidueLevelTask_::allow_noncanonical_aa(
...
      if ( original_residue_type_->variants_match( **aas_iter ) &&

There is a variant matching check. If you start sulfated, ONLY
sulfated variants match and will be allowed. EMPTY does not affect
original_residue_type_ and will have no effect here.

This is perfectly strict variant matching. You require weaker
matching, which ignores mismatches due to *some* variants (sulfated,
etc) and prevents mismatches due to *other* variants (chainbreak,
terminus, etc).

You can try tweaking this check to not care about your subset of
variants: perhaps a flag "allow_design_tofrom_PTMs", and then modify
this check to ignore variant mismatches caused by some curated set of
variants (sulfated, phosphorylated, etc).

You can try removing this check. It will have nasty side effects like
Rosetta will try packing the chainbreak variants or terminus variants
into the middle of the chain. Hopefully the scorefunction will reject
that.



Moving TYR plus S to its own params file as TYS may work. Doug corrects me on the Dunbrack lookup (good). After further
thought, I also realize that Rosetta ignores the PDB standard, in that
it names sulfated tyrosine TYR and adds a sulfate if those atoms are
present, but the PDB uses TYS. So, creating a S-TYR residue type
file, with the name and name3 TYS, would fix your variant matching
problem AND improve the PDB reader to be more standard-compliant.

This may cause the reverse problem, however, where TYR becomes able to
mutate to TYS in all cases. The ResidueLevelTask constructor uses
variant matching just like the troublesome allow_noncanonical_aa
function, and it will let all aa_tyr pass equally (this is how HIS and
HIS_D both work.).

Currently the code distinguishes via "is_protein" and the aa type
being aa_unk - perhaps there is need for a third level of distinction
for chemically modified but not aa_unk residues - they should be
treated with the aa_unk logic.





View Issue Details
270 [Rosetta] Input Handling minor always 2013-05-09 17:12 2013-05-09 17:16
jgray All platforms  
Sergey Any  
normal Any  
assigned  
open  
none    
none  
   
integration tests
./integration.py tests.antib*
allow integration.py to auto-complete tests to run
to make it easier to specify tests
./integration.py tests/antibody -- currently does not work

./integration.py tests/antib* -- this would be very convenient
Select this if your bug report applies to any platform.
There are no notes attached to this issue.





View Issue Details
269 [Rosetta] Bad Coding minor always 2013-05-08 15:04 2013-05-08 19:41
smlewis  
weitzner  
normal  
assigned  
open  
none    
none  
   
get_rosetta.sh
get_rosetta.sh without curl installed
Feature Request, Confirmed As Bug
git get_rosetta.sh non-obviously depends on curl
get_rosetta.sh depends on curl. This is a problem only in that curl is differently distributed from wget. As best I can tell, Linux distros tend to wget and OSX to curl.

get_rosetta.sh should either: A) (preferably) seamlessly use wget instead of curl as necessary, or B) prompt the user to install curl (preferably by activating yum/apt itself)
Notes
(0000286)
smlewis   
2013-05-08 15:07   
As an aside - the script handles the absence of git itself fairly well:

get_rosetta.sh: line 113: git: command not found
get_rosetta.sh: line 140: hash: git: not found
Can't clone! It's likely that git is not installed and/or you are cloning over SSH without SSH keys setup.
See https://help.github.com/articles/error-permission-denied-publickey [^] for instructions on how to setup SSH keys for GitHub.
(0000291)
Sergey   
2013-05-08 19:10   
My vote is for [A] way. I think Brian is responsible for this script, I will forward this to him.





View Issue Details
268 [Rosetta] Crash crash always 2013-05-07 15:20 2013-05-08 17:59
momeara  
renfrew  
normal  
resolved  
fixed  
none    
none Trunk  
   
all
score_jd2.linuxgccrelease -s inputs/1jf8FH.pdb -score:weights mm_std.wts -ignore_unrecognized_res
Confirmed As Bug
1691dfed3fb982744aa0c7c71baf03fad73acccf
K residues causes MMTwist to crash
The K residue type (database/residue_type_sets/fa_standard/residue_types/metal_ions/K.params) has the potassium and two virtual atoms. This leads it to have 3 torsion angles, which are computed and stored in ResidueType::update_derived_data() line 1175. But when scoring with the MMTorsionEnergy score term, the MMTorsionLibrary::lookup() fails with

     No parameters for X-X-X-X.


score_jd2.linuxgccrelease \
  -s inputs/1jf8FH.pdb \
  -score:weights mm_std.wts \
  -ignore_unrecognized_res
1jf8FH.pdb (204,777) 2013-05-07 15:20
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=30&type=bug
1h4xFH.pdb (361,614) 2013-05-07 15:45
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=31&type=bug
Notes
(0000284)
renfrew   
2013-05-08 09:21   
This is actually a problem with the params file; the MMTorsion (mm_twist) code is fully compatible with virtual atoms. This has come up before with the other ions. Folks seem to think that the MMAtomType of "X" is equivalent to a (Rosetta)AtomType of "VIRT" when it is not. The MMTorsion code uses "X" internally as a wildcard value (e.g. X-CT2-CT2-X in the mm_torsion_params.txt would mean use these params for all torsions that have CT2 and CT2 as the central atoms).

The solution is to change the MMAtomType field of the params file for the virtual atoms to be "VIRT" just like it is for the rosetta AtomTypes.
(0000285)
renfrew   
2013-05-08 13:00   
The problem of scoring potassium in 1jf8FH.pdb was fixed by adding potassium params to mm_atom_properties.txt and modifying the params files to reflect the additional atoms types and changing X to VIRT for the virtual atoms.
(0000287)
renfrew   
2013-05-08 15:22   
The 1hxFH.pdb also fails in the MMTorsion lookup but for a different reason. It doesn't contain potassium. It does contain a phosphorlated serine labeled as SEP.

This was a bitch to track down but both...

database/chemical/residue_type_sets/fa_standard/patches/ser_phosphorylated.txt
database/chemical/residue_type_sets/fa_standard/residue_types/ptm-caa/SEP.params

...define a ResidueType with SEP as the three letter code. One has complete MMAtomTypes and the other does not. However even if the MMAtomTypes were fully defined. It probably would have crashed because we don't have MMTOrsion params for phosphate groups.

On a side note, the SEP side chain is missing a hydrogen. I assume that they are built with reduce? That looks like a bug.
(0000288)
momeara   
2013-05-08 15:24   
Should one of those be removed?
(0000289)
renfrew   
2013-05-08 15:35   
So none the params in residue_types/ptm-caa are currently being read in by default. It was the however the first param file I found though and it was really confusing why there were still undefined MMAtomTypes because they are all set in there (they are not set correctly but they are present and not "X"). I later found the patch file that creates the same ResidueType and the MMAtomType were not complete there.

I am not sure who added either of them but one should probably go. I can try to add some torsion params for the phosphate group, pulling them from D/RNA params. To make it work.

When I first made all the NCAA I had params files for most of these phosphorylated and sulfonated residues but CHARMM did not have params for them so I never commited them.
(0000290)
renfrew   
2013-05-08 16:21   
The problem with the phosphoserine in 1h4xFH.pdb was fixed by modifying the patch to add the correct MMAtomTypes. New MMTorsion params were added based on...

Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D. and Lim, C. Structural Characterization of the Phosphotyrosine Binding Region of a High-Affinity aSH2 Domain-Phosphopeptide Complex by Molecular Dynamics Simulation and Chemical Shift Calculations. Journal of the American Chemical Society, 1996, 118: 11265-11277.

...and added to mm_torsions.txt.





View Issue Details
253 [Rosetta] Bad Coding minor always 2013-04-25 13:56 2013-05-07 18:09
momeara  
Sergey  
normal  
feedback  
open  
none    
none  
   
integration.py
cd rosetta_tests/integration && ./integration.py
Confirmed As Bug
r51043 breaks python 2.4 support for rosetta_tests/integration/integration.py
r51043 breaks python 2.4 support for rosetta_tests/integration/integration.py
Notes
(0000257)
jadolfbr   
2013-04-25 14:02   
Do we really need to support Python 2.4 for this?
(0000258)
Sergey   
2013-04-25 15:02   
Hmm os.fork certainly available in python 2.4... Matt what exact error are you getting?
(0000283)
Sergey   
2013-05-07 18:09   
Please post exact error that you are getting while running on Python 2.4





View Issue Details
267 [Rosetta] Documentation minor always 2013-05-04 08:49 2013-05-04 08:49
momeara  
 
normal  
new  
open  
none    
none  
   
all
follow cmake build instructions
Make it more obvious how to use clang with cmake
The description of how to use clang with cmake assumes the use of gcc. Either describe how to make clang work with cmake or perhaps make clang cmake build targets.

There are no notes attached to this issue.





View Issue Details
265 [Rosetta] Incorrect Results minor always 2013-05-03 14:57 2013-05-03 15:18
smlewis  
 
none  
new  
open  
none    
none  
   
docking
docking
Feature Request
Re-create extra docking output (RosettaDock from Rosetta++)
Bug 0000257 covered a discrepancy between the documentation for docking in ROSIE and the actual results. The discrepancy was that the documentation promised a bunch of stuff that Rosetta++ put in the output PDBs that Rosetta3 does not.

The (proper) solution to 0000257 was that the bug was incorrect documentation, not incorrect code behavior, and it was resolved as such. However, I'm sure it would be useful to resurrect at least some of that extra output?
Notes
(0000273)
Sergey   
2013-05-03 15:18   
Good point, extra info might be useful, I am forwarding this to GrayLab...





View Issue Details
257 [ROSIE] Documentation minor always 2013-04-26 16:37 2013-05-03 14:57
smlewis  
Sergey  
normal  
resolved  
fixed  
none    
none  
   
ROSIE docking
ROSIE docking
Confirmed As Bug
4e55781
ROSIE docking results do not list any of the "extra data" suggested in the documentation
ROSIE docking documentation (http://rosettadock.graylab.jhu.edu/documentation/docking [^]) lists 9 things in the result PDBs: coordinates, scores, and a bunch of processed scores (cross-interface contacts, etc). None of these beyond the normal coordinates and scores are actually in the result PDBS: http://rosettadock.graylab.jhu.edu/fs/2426/output/proteins.ppk_0013.pdb [^]
Notes
(0000262)
Sergey   
2013-04-26 23:16   
Could this 'extra data' be found in score file? (Because we do provide it)
(0000265)
smlewis   
2013-04-29 09:22   
It's not in the score file, it's not in the logs. It's not present when you run Rosetta by itself (like in the integration tests, etc). I can't find it as a sub-page anywhere (here's a test example: http://rosettadock.graylab.jhu.edu/docking/viewjob/2426 [^]).

Where did you get the examples from for the documentation? Is it ported from RosettaDock? Is it possible it's Rosetta++ documentation?
(0000268)
Sergey   
2013-04-30 15:08   
Ah, this is correct: the docs was taken from Rosetta++ version. I have remove that extra parts [1-9] that you mention. Thanks Steven!





View Issue Details
264 [Rosetta] Website error minor always 2013-05-03 13:12 2013-05-03 13:58
rmoretti  
Sergey  
normal  
resolved  
fixed  
none    
none  
   
none
na
00000
RSS feed still lists svn link
The Rosetta Tests RSS feed at http://rosettatests.graylab.jhu.edu/rss [^] is still giving a link to the svn server changeset, rather than the Github changeset.
Notes
(0000272)
Sergey   
2013-05-03 13:58   
Should be fixed now. Please note that most RSS readers will cache stuff so you will need to wait until new revision appear before changes shown.





View Issue Details
262 [Rosetta] Input Handling minor always 2013-05-01 11:09 2013-05-01 11:09
nannemdp X86  
smlewis Linux  
normal CentOS  
assigned Trunk  
open  
none    
none  
   
format_converter, score_jd2, probably all other jd2 apps
rosetta_source/bin/format_converter.default.linuxgccrelease -database rosetta_database -no_optH -in:file:silent SILENT.silent.gz -out:pdb -out:no_nstruct_label
only first model read from gzipped silent files
The job distributor is only reading the first model of gzipped silent files, using in:file:silent SILENT.silent.gz. Unzipping the silent file and reading again will read all the models in the silent file. This was observed with both the format_converter and score_jd2.
Create a multi-model gzipped silent file.
Unsuccessfully extract models with format_converter:
rosetta_source/bin/format_converter.default.linuxgccrelease -database rosetta_database -no_optH -in:file:silent SILENT.silent.gz -out:pdb -out:no_nstruct_label
Unzip silent file
Successfully extract models with format_converter:
rosetta_source/bin/format_converter.default.linuxgccrelease -database rosetta_database -no_optH -in:file:silent SILENT.silent -out:pdb -out:no_nstruct_label
There are no notes attached to this issue.





View Issue Details
260 [Rosetta] Incorrect Results major always 2013-04-29 11:12 2013-04-29 11:51
smlewis  
renfrew  
normal  
assigned  
open  
none    
none  
   
make_rot_lib
make_rot_lib
make_rot_lib guts lost in warning-removal drive
This commit:

https://svn.rosettacommons.org/trac/changeset?reponame=&new=54323%40trunk%2Frosetta%2Frosetta_source%2Fsrc%2Fapps%2Fpublic%2Fncaa_utilities%2Fmake_rot_lib.cc&old=46710%40trunk%2Frosetta%2Frosetta_source%2Fsrc%2Fapps%2Fpublic%2Fncaa_utilities%2Fmake_rot_lib.cc [^]

appears to remove an important part of make_rot_lib. Also, Doug, you mentioned curiosity that the integration tests hadn't gotten very angry about this.
There are no notes attached to this issue.





View Issue Details
261 [Rosetta] Bad Coding minor always 2013-04-29 11:44 2013-04-29 11:44
smlewis  
bborgo  
normal  
assigned  
open  
none    
none  
   
VIP
VIP -resfile does_nothing.resfile
Feature Request
VIP request: at least minimal resfile respect
It would be nice if VIP respected resfiles, *especially* because it will throw resfile-related errors because it uses the APOLAR ResfileCommand internally. See this thread: https://www.rosettacommons.org/node/3268 [^]
There are no notes attached to this issue.





View Issue Details
259 [Rosetta] Bad Coding minor always 2013-04-29 10:00 2013-04-29 10:00
smlewis  
bborgo  
normal  
assigned  
open  
none    
none  
   
VIP
VIP -s pdb_with_ligands.pdb
VIP uses nonstandard PDB reader
VIP appears to be using a nonstandard PDB reader (core::io::pdb::build_pose_from_pdb_as_is) instead of the standard (core::import_pose::pose_from_pdb). Is this for a reason? See also this user error:

https://www.rosettacommons.org/node/3268#comment-6112 [^]
There are no notes attached to this issue.





View Issue Details
255 [Rosetta] Incorrect Results minor always 2013-04-25 19:18 2013-04-28 17:40
amelie All platforms  
amelie Any  
normal Any  
resolved Trunk  
fixed  
none    
none  
   
loopmodel.<binary>
loopmodel.<binary> -loops:remodel perturb_kic -loops:refine refine_kic
Confirmed As Bug
55062
KIC always reports a chainbreak score of 0
The chainbreak score term of the scorefxn used for repacking must have gotten lost in some repacking step, so that now the reported chainbreak score is always 0.
Select this if your bug report applies to any platform.
Notes
(0000260)
smlewis   
2013-04-25 21:05   
If the chainbreak score is reported, the score is working - the problem is the protein_cutpoint_upper and _lower variant types on the expected break are lost. chainbreak is only calculated over peptide bonds with those variants (and a break in the FoldTree/AtomTree to go with it, or else the variants cannot be added - since KIC has no break, it might never work).
(0000261)
amelie   
2013-04-25 21:14   
Steven - this was probably a misunderstanding, the chainbreak score is not reported during the course of loop modeling, only at the very end of the protocol where it is explicitly requested via getPoseExtraScores. When using sfxn->show(pose) there is no chainbreak score shown. The upper and lower cutpoints are set though. As soon as I set a non-zero weight for chainbreak, there is a non-zero score.
(0000263)
amelie   
2013-04-28 17:33   
resolved in r55062





View Issue Details
232 [Rosetta] Incorrect Results major always 2013-03-26 12:18 2013-04-28 17:36
tjacobs2 All platforms  
amelie Any  
high Any  
assigned Trunk  
open  
none    
none  
   
LoopModeling, anything else that uses KIC
-s pdb_with_broken_loop.pdb -loops:remodel perturb_kic -in:file:fullatom -loops:fast -nstruct 1 -overwrite -kic_leave_centroid_after_initial_closure
Confirmed As Bug
Kinematic Closure broken with extended loops (and possibly even without them)
Kinematic Closure has a severe bug that causes failure to model loops with previously unclosed loops.
1)Run loop modeling application on a loop that starts out broken
2)Observe that the loop is still broken after a "successful" KIC closure
The bug looks like it is due to the implementation of the idealize_loop_first logic in KinematicMover.cc. The code calls conformation::idealize_position(), which does NOT idealize residues at cutpoints in the FoldTree. This is a major problem because then the bond/angles and lengths given to the BridgeObjects function don't match the pose, and are never applied (only the torsions from the solution are applied, even though the set_pose_after_closure function of the perturber takes the bond angles and lengths, it ignores them). Another potentially major problem (which can happen even when starting with a closed loop) is that the perturb_chain() function of the perturber is allowed to modify the bond angles and lengths prior to calling BridgeObjects, but doesn't actually change the pose (it can't, it's given a const reference). This means that, once again, the bond angles/lengths given to the BridgeObjects function don't match the pose and are never mapped back, which can lead to a broken loop.

It's easiest to reproduce this bug using perturb_kic with the kic_leave_centroid_after_initial_closure flag on (which causes this to run very quickly, and also prevents the monte-carlo wrapper around this call from keeping only solutions that happen to be closed).

Probably the easiest way to fix this is to make sure that *everything* returned by the BridgeObjects function (which, in the case of angles/lengths is identicle to what is passed in, which makes me wonder why even bother returning them...) is actually applied to the pose afterwords.
Select this if your bug report applies to any platform.
Notes
(0000264)
amelie   
2013-04-28 17:36   
Partly resolved in r55062.
Note that the parent KinematicPerturber does not know about the possibility to vary bond angles. Thus their overwriting is only implemented in the inherited specific perturbers.
The issue of occasional open conformations remains.





View Issue Details
252 [Rosetta] Input Handling minor always 2013-04-22 19:58 2013-04-22 23:06
rmoretti  
 
normal  
new Trunk  
open  
none    
none  
   
any resfile reading ones
-resfile misnumbered.resfile
Issues with error message reporting (resfiles)
If you have an error in a resfiles, Rosetta apparently no longer prints out the reason for the error. It simply prints "ERROR:: Exit from: src/core/pack/task/ResfileReader.cc line: 1488" - despite having a tracer output statement for the message (with endl) just before the output.
Run a protocol with a bad resfile (e.g. with a residue that doesn't exist)
I'm not sure if this is a bug in Rosetta, or it's more some issue with stream flushing on my local machine. (Note that this has been run directly in the terminal.)

I'm also not sure if it's resfile-reading specific, or a more general issue.
Notes
(0000255)
amelie   
2013-04-22 20:19   
I have experienced the same issue a few weeks ago, on multiple machines, so I don't think it's a local issue.
(0000256)
Sergey   
2013-04-22 23:06   
If std::endl is present at the end of Tracer output then string should be flushed as soon as operator execute, so this most likely not the std::cout flushing issue.





View Issue Details
250 [Rosetta] Input Handling minor always 2013-04-12 13:37 2013-04-12 19:06
rmoretti  
rmoretti  
normal  
resolved Trunk  
fixed  
none    
none Trunk  
   
rosetta_scripts
rosetta_scripts
54830
RosettaScripts can't recognize true and false
For an XML tag attribute which takes a boolean, you can't use the strings "true" or "false" to set the value - you have to use 0 or 1.

This is confusing as the RosettaScripts documentation often uses the strings "true" and "false" to describe default settings.

It also is different behavior from the commandline booleans, which can take a number of different strings to represent true and false.
There are no notes attached to this issue.





View Issue Details
251 [Rosetta] Website error minor always 2013-04-12 13:57 2013-04-12 14:46
smlewis  
Sergey  
low  
assigned  
open  
none    
none  
   
email changelogs
N/A
Feature Request
New git changelogs have no clickable trac link
The new git email changelogs look like this:


commit 9ab01e707c1545e8370f503047d339eebee0c8a0
Author: fcchou <fcchou@6189c7af-7406-0410-a2ce-f22f51069c23>
Date: Fri Apr 12 00:50:50 2013 +0000

    update rna_helix.py

    git-svn-id: https://svn.rosettacommons.org/source/trunk/rosetta@54797 [^] 6189c7af-7406-0410-a2ce-f22f51069c23

M rosetta_tools/rna_tools/pdb_util/rna_helix.py


It would be nice if that https:// was actually a clickable link (in this case, https://svn.rosettacommons.org/trac/changeset/54797 [^] ). I recognize that it may be a waste of time to upgrade this given the pending switch to git.

It would also be nice if the changelog inserted a break between log entries (like ---------------------------------------) to make the break between entries more obvious.
Notes
(0000252)
smlewis   
2013-04-12 13:58   
The single-email change notifications have the same link formatting problem.
(0000253)
delucasl   
2013-04-12 14:31   
(edited on: 2013-04-12 14:31)
git-svn-id lines are actually inserted by the git-svn infrastructure, and are parsed by git-svn to figure out how to handle fetches properly. While we could use filter-branch to rewrite all the past commits, I'm not sure this is a good idea. in 3 weeks, we'll be switched over to an entirely git based system, at which point the svn metadata will become a lot less important.

In short, this is something that can be done, but It would potentially complicate matters significantly. We'll be done with svn in 3 weeks or so anyways, I hope.

edit: we can make the test server emails have clickable links to github

(0000254)
Sergey   
2013-04-12 14:46   
I will take care of this after we move to GitHub. Right now I can make it clickable to github but it will point to Brian private repository and there is little use of that since most of the people are could not see it.





View Issue Details
248 [Rosetta] Crash minor always 2013-04-11 14:30 2013-04-11 17:40
smlewis  
Sergey  
normal  
assigned  
open  
none    
none  
   
integration test
integration.py this_test_has_no_command_file
Feature Request, Confirmed As Bug
integration.py handles missing command files poorly
Create a test directory within integration/tests with no command file.

integration.py will fail with something like:
Traceback (most recent call last):
  File "integration.py", line 1011, in <module>
    sys.exit(main(sys.argv[1:]))
  File "integration.py", line 264, in main
    cmd_line_sh, workdir = generateIntegrationTestCommandline(test, outdir);
  File "integration.py", line 671, in generateIntegrationTestCommandline
    cmd += file(path.join(workdir, "command")).read().strip()
IOError: [Errno 2] No such file or directory: '/home/sml58/git_rosetta/rosetta_tests/integration/new/ccd_loop_terminal/command'

It is correct in that it knows the command file doesn't exist, but it should probably catch the nonexistence of the file and handle it as a permafail test, instead of crashing integration.py.

Additionally, child processes of integration.py are NOT KILLED when it dies in this fashion - so if you're running at -j8, your other 7 don't die immediately. They should be killed when integration.py dies. Maybe that's a separate bug. I guess integration.py does not need to die here anyway.
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View Issue Details
249 [Rosetta] Incorrect Results minor always 2013-04-11 15:14 2013-04-11 15:14
smlewis  
 
normal  
new 3.4  
open  
none    
none  
   
minirosetta -protocol threading
minirosetta -protocol threading
-select_best_loops_from associated with ludicrous models (user report for 3.4)
https://www.rosettacommons.org/node/3231#comment-6032 [^]

Basically, this user has a command line and input set (command line is in thread) that results in some reasonable models, and some models with broken sidechains - CB-xG bond vector distances are 20 angstroms or more.

The user reports that the problem is more frequent with larger values of -select_best_loops_from. This implies to me that something is remembering rotamers/sidechains/atom coordinates it should not, and re-threading wrong rotamers after some centroid-fullatom step.
There are no notes attached to this issue.





View Issue Details
230 [Rosetta] Crash major always 2013-03-25 09:05 2013-04-11 15:14
smlewis  
smlewis  
high  
new All  
open  
none    
none  
   
loop_model
loop_model -perturb perturb_ccd
LoopMover_CCD (perturb_CCD) does not allow terminal loops; appears to be typo
https://www.rosettacommons.org/node/3231#comment-5952 [^]

The line of code in question:
    runtime_assert( !loop.is_terminal( pose ) || pose.fold_tree().is_cutpoint( loop_cut ) );

LoopMover_CCD.cc:212

I think this is a bug and is_terminal should not be negated...there are several other is_terminal checks in this code that all suggest the Mover works just fine with terminal loops; Tim agrees.
Notes
(0000215)
smlewis   
2013-03-25 09:56   
It appears that with an invalid cutpoint, the cutpoint auto-setter picks the thing that is already a cutpoint (the terminus), which normally lets this assert pass - except that the downstream code never actually modifies the loop. (oops.)

With a valid (but unused) cutpoint, the assertion fails.
(0000216)
smlewis   
2013-03-25 10:38   
After repairing the assertion, the code appears to simply do nothing. I modified the 4fxn-based ccd-based loop_closure test (including changing to -loops:remodel perturb_ccd from quick_ccd) to use a terminal loop...but "for all fragments" loop

for ( std::vector< FragmentMoverOP >::const_iterator it = fragmover.begin(),it_end = fragmover.end(); it != it_end; it++ ) {

never gets entered for some reason.
(0000217)
smlewis   
2013-03-25 10:39   
unassigning





View Issue Details
91 [Rosetta] Incorrect Results minor always 2012-08-30 13:31 2013-04-10 19:17
Labonte  
Sergey  
low  
resolved Trunk  
fixed  
none    
none  
   
any using PyMolMover or inheriting from it
See Steps To Reproduce Above
54768
PyMolMover.energy_type() and/or ScoreType enum problem
If one sets the energy type of a PyMolMover (the C++ version, not the Python version, from which the latter inherits) to total_score using PyMolMover.energy_type(total_score), the energy type is instead set to end_of_score_type_enumeration, (which is also the default setting).

All other ScoreTypes work correctly.
In [1]: from rosetta import *

In [2]: init()

In [3]: pymol = PyMolMover()

In [4]: pymol.energy_type()
Out[4]: rosetta.core.scoring.__scoring_all_at_once_.ScoreType.end_of_score_type_enumeration

In [5]: pymol.energy_type(fa_atr)

In [6]: pymol.energy_type()
Out[6]: rosetta.core.scoring.__scoring_all_at_once_.ScoreType.fa_atr

In [7]: pymol.energy_type(total_score)

In [8]: pymol.energy_type()
Out[8]: rosetta.core.scoring.__scoring_all_at_once_.ScoreType.end_of_score_type_enumeration

In [9]: pymol.energy_type(end_of_score_type_enumeration)

In [10]: pymol.energy_type()
Out[10]: rosetta.core.scoring.__scoring_all_at_once_.ScoreType.end_of_score_type_enumeration
Notes
(0000245)
rmoretti   
2013-04-02 19:05   
It probably should be noted that end_of_score_type_enumeration *is* total_score, at least as far as the C++ enumeration is concerned. In core/scoring/ScoreType.hh where the enumeration values are defined, they're explicitly set as equal.

I think the issue, if there is any, is not so much that the value isn't being set appropriately, but rather that the representation of that enumeration value at the Python level is "ScoreType.end_of_score_type_enumeration", rather than "ScoreType.total_score" (Note that the name strings as accessed through the ScoreTypeManager shouldn't suffer this problem.)
(0000250)
Labonte   
2013-04-10 15:15   
Ok, not really a bug then, but I still think it is a potential issue of confusion for end users of PyRosetta. Maybe there is a way to intercept it at the Python end to make it more clear to users....
(0000251)
Sergey   
2013-04-10 19:15   
(edited on: 2013-04-10 19:16)
Just committed fix for this (r54768). Please see if it works for you.






View Issue Details
242 [ROSIE] Website error minor always 2013-04-03 12:04 2013-04-09 19:21
smlewis  
Sergey  
low  
resolved  
fixed  
none    
none  
   
N/A
N/A
Confirmed As Bug
72b2597ee4599e6553bb448b9b13b8025f8bb776
erraser on ROSIE has "in press" citation but paper is out
The paper came out: Nat Methods. 2013 Jan;10(1):74-6. doi: 10.1038/nmeth.2262. Epub 2012 Dec 2.
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View Issue Details
246 [Rosetta] Incorrect Results major always 2013-04-06 00:21 2013-04-06 00:25
amelie X86  
Linux  
normal CentOS  
new Trunk  
open  
none    
none  
   
all, presumably
rosetta_source/bin/fixbb.linuxgccrelease -database rosetta_database/ -ignore_unrecognized_res -packing:repack_only -score:weights score12 -s 1abc.pdb
energy tables aren't calculated before loading the input structure when using -score:weights score12
When running with "-score:weights score12" on linux, energy tables are only calculated after a structure has been read in, leading to all initial scores being 0 (and weird repacking results). In contrast, when running with "-score:weights score12.wts", energy tables are calculated before the input structure is loaded.

See change in position of the following lines, and the difference in the .sc files:

core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.


## -score:weights score12
SEQUENCE:
SCORE: total_score description
SCORE: 0.000 no_extension1a0q_clean_0001

## -score:weights score12.wts

SCORE: total_score dslf_ca_dih dslf_cs_ang dslf_ss_dih dslf_ss_dst fa_atr fa_dun fa_intra_rep fa_pair fa_rep fa_sol hbond_bb_sc hbond_lr_bb hbond_sc hbond_sr_bb omega p_aa_pp pro_close rama ref description
SCORE: 238.616 0.336 12.699 4.605 16.641 -1468.125 248.057 3.242 -33.495 934.874 702.679 -28.539 -205.402 -10.467 -22.163 66.117 -32.967 88.126 28.937 -66.540 with_extension1a0q_clean_0001
rosetta_source/bin/fixbb.linuxgccrelease -database rosetta_database/ -ignore_unrecognized_res -packing:repack_only -score:weights score12 -s 1abc.pdb

and

rosetta_source/bin/fixbb.linuxgccrelease -database rosetta_database/ -ignore_unrecognized_res -packing:repack_only -score:weights score12.wts -s 1abc.pdb -
On (my) Mac it doesn't make a difference whether the .wts extension is given or not.

For -score:weights soft_rep_design, properly initialized energy tables and scored structures are generated independent of whether .wts was included on the machine affected by the -score:weights score12 issue.
fixbb.linux.score12.log (9,284) 2013-04-06 00:23
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=26&type=bug
fixbb.linux.score12.wts.log (9,385) 2013-04-06 00:25
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=27&type=bug
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View Issue Details
245 [Rosetta] Incorrect Results major always 2013-04-04 16:28 2013-04-04 16:35
AndrewLeaverFay All platforms  
AndrewLeaverFay Any  
high Any  
resolved All  
fixed  
none    
none Trunk  
   
all
I wrote a unit test which will go in with the fix.
Confirmed As Bug
54685
Context-dependent, one-body energies not scored during minimization
Context-dependent, one-body energies (cd1b) were not being added to the minimization graph and these terms were not reporting scores during minimization, though, some of them were reporting derivatives, leading to score/derivative mismatches. This bug has been in place since r38314, 3 years ago.
Select this if your bug report applies to any platform.
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View Issue Details
234 [Rosetta] Input Handling minor always 2013-03-28 09:56 2013-04-04 16:33
smlewis  
renfrew  
normal  
resolved  
fixed  
none    
none Trunk  
   
scons
scons mode=A,B vs. mode=B,A
Confirmed As Bug
54684
if you use multiple extras options, SCons does not order consistently
pasted from a list email from Doug Renfrew:

Also, for those who may be unaware, if you use multiple extras options, keeping them in the same order will avoid a lot of headache. For example...

./scons.py mode=release extras=mpi,static bin
./scons.py mode=release extras=static,mpi bin

produces two different directory hierarchies in rosetta_source/build. You will end up with two sets of binarys and end up doing two compiles.

This should probably be a bug. It could be fixed if scons would sort the extras list alphabetically.

Notes
(0000220)
Sergey   
2013-03-28 11:40   
If anyone know the place where extras is process: just use sorted(<extra list>) so it always the same...
(0000221)
renfrew   
2013-03-28 11:45   
I am about to commit that change
(0000222)
renfrew   
2013-03-28 13:17   
I have decided not to commit this yet.

Changing line 255 in rosetta_source/tools/build/setup.py from...
"-".join(options.extras)

...to simply...

"-".join(sorted(options.extras))

Prevents the creation of duplicated paths and different executable names, but a...

./scons.py mode=debug extras=static,mpi

...followed by a...

./scons.py mode=debug extras=mpi,static

...results in a full recompile.

Scons thinks they are different targets, I think.
(0000223)
renfrew   
2013-03-28 13:24   
I do not currently know how scons decides what needs to compiled and what does not need to be compiled. But I suspect that also needs to be changed. I am unassigning this from myself since I suspect I can be of no more help.
(0000235)
rmoretti   
2013-04-01 19:01   
Line 180 in rosetta_source/tools/build/setup.py probably also needs to change

Or better yet, sort the options.extras where there loaded in the setup_build_options() function in the same file. Probably about line 128, where "default" is set as the default extras tag.
(0000243)
renfrew   
2013-04-02 17:21   
(edited on: 2013-04-02 17:33)
So I guess I lied about trying to be more help. This patch seems to do the trick
[code]
diff --git a/rosetta_source/tools/build/setup.py b/rosetta_source/tools/build/setup.py
index f48b502..cc34a5d 100644
--- a/rosetta_source/tools/build/setup.py
+++ b/rosetta_source/tools/build/setup.py
@@ -125,7 +125,9 @@ directory it is built to, and what settings it ultimately uses.

     # Nothing special is currently done to select mode, kind or extras
     if len(actual.extras) == 0:
- actual.extras.append("default")
+ actual.extras.append("default")
+ else :
+ actual.extras.data.sort()

     return requested, actual
[/code]






View Issue Details
244 [Rosetta] Incorrect Results minor always 2013-04-04 11:08 2013-04-04 11:08
jecorn All platforms  
smlewis Any  
normal Any  
assigned All  
open  
none    
none  
   
minirosetta
all
minirosetta app incorrectly uses -out:user_tag option
Various apps read the -out:user_tag option differently. For example, minirosetta adds the value of the option to the structure/description tag, whereas rosetta_scripts adds it as a new field in the score/silent file. Since the -out:prefix and -out:suffix options already take care of appending data to the structure tag, the minirosetta app should be changed to mimic rosetta_scripts (per Mike Tyka)
Select this if your bug report applies to any platform.
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View Issue Details
243 [Rosetta] Documentation minor always 2013-04-04 11:04 2013-04-04 11:08
jecorn All platforms  
smlewis Any  
normal Any  
assigned  
open  
none    
none  
   
all
all
Incorrect documentation of -out:user_tag option
-out:user_tag documentation states, "add this tag to structure tags: e.g., a process id". This is the behavior for some applications (e.g. minirosetta), but not for others (e.g. rosetta_scripts).

In bug id 0000231 Mike Tyka decided this behavior should actually be part of -out:prefix and -out:suffix, and that -out:user_tag should instead add a new field to silent/score files and not add to the structure tag. The documentation for user_tag should be changed to reflect this.

Inconsistent behavior of the minirosetta app will be filed separately.
Select this if your bug report applies to any platform.
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View Issue Details
231 [Rosetta] Incorrect Results minor always 2013-03-25 12:36 2013-04-04 11:08
jecorn All platforms  
mtyka Any  
normal Any  
resolved Trunk  
no change required  
none    
none Trunk  
   
rosetta_scripts
rosetta_scripts.linuxgccrelease -out:file:silent_struct_type binary -out:file:silent out.out
-
-out:user_tag option only sometimes obeyed
The -out:user_tag option is documented as adding a user-generated id to structure tags in silent files. This can be very useful for uniqueifying tags across multiple processes (e.g. adding a process ID), simplifying grepping of structures from the silent files.

This behavior works with some apps and not with others. The minirosetta app can write both text and binary silent files such that the silent files have both a new field called "user_tag" and the user_tag is added to the "description field" (S_<user_tag>_####). However, rosetta_scripts (which solely uses binary silent files) writes silent files with the "user_tag" field, but the user_tag is NOT added to the structure tag.

Both minirosetta and rosetta_scripts use jd2. However, minirosetta uses a specialized BOINCJobDistributor. Is this part of the cause? Or is there something special about the rosetta_scripts silent file handling that forgets to check for user_tag?
Run minirosetta app app "-out:user_tag 1" and either -out:file:silent_struct_type protein (default) or -out:file:silent_struct_type binary. Marvel at the user_tag in the description (S_1_00000001)

Run rosetta_scripts with "-out:user_tag 1" (default/only behavior is -out:file:silent_struct_type binary) and cringe at the lack of user_tag in the description (S_0001).
Select this if your bug report applies to any platform.
Notes
(0000248)
mtyka   
2013-04-04 01:55   
[working as intended]

Looks like user_tag is behaving as designed - it's not supposed to be added to the tag. It is only supposed to show up as an extra field. If the user_tag is showing up in the decoy_tag in minirosetta app then that's a seperate bug.

The flag you want is -out:prefix (or -out:suffix) and does exactly what you wanted - it modifies the decoy_tag and works just fine in rossetta_scripts.
(0000249)
mtyka   
2013-04-04 01:59   
Working as intended.

Correct option to modify decoy_tag is -out::prefix and -out::suffix





View Issue Details
240 [Rosetta] Incorrect Results major always 2013-04-02 16:21 2013-04-03 12:29
Labonte All platforms  
pbradley Any  
normal Any  
resolved Trunk  
fixed  
none    
none Trunk  
   
DNA & RNA applications?
N/A
54660
abs() method used on Real values in core::scoring
This may not be an error, but I'd like someone who knows more to double check it, just in case, because it looks very wrong to me and is throwing a ton of warnings.

In core/scoring/dna/base_geometry.cc, a lot of asserts are using the int abs(int) method but passing Reals. Rather than just cast everything to an int, I wanted to make sure that this is the intended behavior, because there is also a float abs(float) (in a different namespace, cmath) that could be used.

For an example, see l. 1246:

assert( abs( params[1] - asin( dot( MBT.col_z(), cross( M2.col_y(), M1.col_y() ) ) ) ) + abs( params[1] - asin( dot( MBT.col_z(), cross( M2.col_x(), M1.col_x() ) ) ) ) < 1e-2 );

where params is a vector1<Real>.

Not all of the issues are in asserts either -- l. 1303:

Real dot = std::abs( n12.dot( ( atoms[4]-atoms[3] ).normalized() ) );

where n12 is an xyzVector. This looks very bad to me; or am I missing something?

No one listed him- or herself as author on this file, but whoever you are, could you fix all the abs() calls in this file, whether by casting or by using cmath::abs()? Thanks!
http://www.cplusplus.com/reference/cstdlib/abs/ [^]
Select this if your bug report applies to any platform.
Notes
(0000242)
rmoretti   
2013-04-02 16:41   
Note: For those who have trouble finding it, the file is core/scoring/dna/base_geometry.cc

My guess would be this is a potential bug due to unawaredness that the abs function doesn't have sane polymophism.

svn praise (aka svn blame) and the svn server places most to the initial commits of the code by Phil Bradley some 6 years ago. Given that he's still actively working on code that likely uses these functions, I'd recommend shooting him an email directly.
(0000244)
Labonte   
2013-04-02 17:37   
Thanks, Rocco!
(0000247)
pbradley   
2013-04-03 12:29   
Thanks for the tip! Switched to std::fabs and included <cmath> in revision 54660





View Issue Details
85 [PyRosetta] Input Handling major always 2012-08-21 17:41 2013-04-03 11:15
jecorn  
evanbaugh  
normal  
assigned  
open  
none    
none  
   
PyRosetta
all
Pyrosetta pose_from_rcsb assumes dimer
pose_from_rcsb (the called cleanCRYS method) seems to assume that an input PDB is a dimer containing two chains of different sequence. So importing 1YY8 (the stock PyRosetta example) works, since it takes a crystal tetramer into a biologically relevant dimer. But importing 1UBQ (or any other monomer) crashes with an error about "not a 2.0-mer", unless CRYS=False is provided. So the current implementation will not monomerize an incoming pdb structure that contains multiple copies with identical sequence.

This behavior is not documented.

Since most Rosetta work is done with monomers, it might make more sense to default to monomer input (removing other members of the AU), and allow the user to specify multimers to pass to cleanCRYS. This could be done by modifying pose_from_rcsb to take a *-mer int as an argument, then passing that on to cleanCRYS.
Notes
(0000080)
jecorn   
2012-08-22 10:30   
The easiest fix for this might be to just dump *.mono.pdb regardless of whether or not the the oligomer argument to cleanCRYS is correct. This doesn't fix much, but at least prevents pose_from_rcsb from crashing.

./rosetta/__init__.py
426a427
> pose.dump_pdb(pdb_file[:-4]+'.mono.pdb')
(0000081)
evanbaugh   
2012-08-22 10:44   
cleanCRYS should be deprecated within the week, it was never fully tested and uses a very hacky method to assess identical chains
in any case, cleanCRYS should have an input for specifying the size to check (i.e. 2 for monomer, 3 for trimer, etc.) which defaults to 2
pose_from_rcsb has the "CRYS" option- but it doesn't allow you to specify size so in this context it really means "check for a dimer of sequences"
you should be able to use
load_from_rcsb
cleanATOM
cleanCRYS
pose_from_pdb
to accomplish what you want
a much fancier version of this should be available soon
sorry for the confusion, I'll close this out once its officially deprecated
(0000114)
jecorn   
2012-10-04 18:59   
Reminder sent to:: evanbaugh
Hi Evan. Any progress on this?
(0000137)
jecorn   
2013-01-04 13:09   
Hi evan. Still wondering about this bug... I'm teaching a PyRosetta class using non-dimers, and it's causing some problems.
(0000246)
jecorn   
2013-04-03 11:15   
Reminder sent to:: evanbaugh
ping





View Issue Details
158 [Rosetta] Bad Coding minor always 2012-12-08 12:06 2013-04-02 18:19
Labonte All platforms  
honda Any  
high Any  
resolved Trunk  
fixed  
none    
none Trunk  
   
unknown
N/A
54161
value -1 assigned to Size variable
While cleaning Rosetta of warnings, I came to
/rosetta_source/src/protocols/forge/remodel/RemodelWorkingSet.cc, line 427,
where we find the following code:
core::Size head = -1, tail = -1, headNew = -1, tailNew = -1; //safety, init to negative values

This line itself does not throw a warning; however, it triggers several others further down, and I'm pretty sure it's not kosher to assign a negative value to an unsigned integer.

Could someone who wrote or knows more about this code take care of this for me? Thanks!
Select this if your bug report applies to any platform.
Notes
(0000184)
Labonte   
2013-03-17 19:32   
Anyone?
(0000185)
smlewis   
2013-03-18 13:25   
svn blame suggests you need to talk to Pos-su Huang and Ron Jacak.





View Issue Details
241 [Rosetta] Incorrect Results minor always 2013-04-02 16:29 2013-04-02 16:33
smlewis  
 
normal  
new  
open  
none    
none  
   
docking_protocol
docking_protocol -docking_local_refine -cst_file
Confirmed As Bug
Docking uses constraints only on first nstruct with -docking_local_refine
This test works with the docking_full_protocol integration test. (and attached)

-s input/1brs.pdb
-out:file:scorefile 1brs.fasc
-out:file:fullatom
-nstruct 3

-constraints:cst_file constraints.txt

-docking_local_refine


This flag set causes constraints to be used only on the first nstruct but not later nstruct. atom_pair_constraint weight is 1 in all outputs so I assume the constraints aren't getting loaded in subsequent nstruct - probably a bug in something getting remembered that shouldn't.


-reinitialize_mover_for_each_job fixes the problem but doesn't seem the right solution.
https://www.rosettacommons.org/node/3247 [^]
docking.tar.gz (224,149) 2013-04-02 16:33
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=25&type=bug
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View Issue Details
239 [Rosetta] Bad Coding minor always 2013-04-02 15:25 2013-04-02 15:25
smlewis  
smlewis  
normal  
assigned  
open  
none    
none  
   
erraser / rna_rosetta_ready_set.py
erraser / rna_rosetta_ready_set.py -rna_prot_erraser true
rna_rosetta_ready_set.py does not alter protein hydrogen names for consistency
rna_rosetta_ready_set.py was altered to allow protein via -rna_prot_erraser, but it does not rename hydrogens for protein residues. This means Rosetta ignores and recreates those hydrogens, which will have deleterious downstream effects.
Ideally we'll just fix the hydrogen names in the parameters files in the long term...in the short term this is probably worth patching
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View Issue Details
238 [Rosetta] Crash major always 2013-04-02 11:39 2013-04-02 13:54
kimdn  
momeara  
normal  
feedback Trunk  
reopened  
none    
none Trunk  
   
cluster.default.linuxgccrelease
cluster.default.linuxgccrelease @/nas02/home/k/i/kimdn/commands/flag_cluster
54637
Incompatibility between new sp2+hackelec and cluster
with

-corrections:hbond_sp2_correction
-score:weights sp2_correction.wts

in option file (in an effort to use new sp2+hackelec potential), it crahses

"basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 6400 residue types
core.pack.task: Packer task: initialize from command line()
Segmentation fault"

without options

-corrections:hbond_sp2_correction
-score:weights sp2_correction.wts

in option file (in an effort not to use new sp2+hackelec potential), it doesn't crash
"basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 6400 residue types
core.pack.task: Packer task: initialize from command line()
core.pack.dunbrack: Dunbrack library took 0.03 seconds to load from binary
protocols.cluster: RESCORING: S_00098130_from_1_1_0047.pdb
protocols.cluster: Adding struc: 2.122e-314"

I attach a flag file that I used.

(As a record,,,,,

3k pdb files -> seg fault
while 1k pdb files -> ran well)

flag_cluster (318) 2013-04-02 11:39
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=24&type=bug
Notes
(0000238)
momeara   
2013-04-02 12:13   
Adding

-corrections:hbond_sp2_correction
-score:weights sp2_correction.wts

to the cluster integration test does not segfault. Doonam, can you please either add or link all the input files so that I can reproduce the segfault?
(0000239)
rmoretti   
2013-04-02 12:51   
It looks like it's a issue with the Dunbrack library.

-corrections:hbond_sp2_correction turns on the dun10 library. If for some reason you had a corrupt dun10 library, that could account for the crash with the flag, but no crash without the flag (i.e. using dun02).

Make sure your database is up-to-date and matches the files on the server (i.e. svn status doesn't report any changed), and try deleting the generated dun10 binary (e.g. rosetta_database/rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin), if any. (Keep a copy of the binary for later post analysis - we should give an error message if the binary is corrupt, rather than a segfault.)

The other thing is if you're running this on multiple processors/threads, you may be encountering write collisions with generating the dun10 binary for the first time. Try doing a single-processor single-threaded score with the -corrections:hbond_sp2_correction to pre-generate the binary prior to launching a multiprocessor/multithreaded cluster run.
(0000240)
kimdn   
2013-04-02 13:40   
After reading rocco's note, I erased
"rosetta_database/rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin"

and ran cluster again and this time it ran well like below.

Since 'Dunbrack10.lib.bin_led_seg_fault_compiled_at_54637' is too big, I copy the file into Kuhlman lab's internal site. (@ contador /home/kimdn/scr/data/do_not_erase/Dunbrack10.lib.bin_led_seg_fault_compiled_at_54637)

"core.pack.task: Packer task: initialize from command line()
Warning: Unable to locate database file rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin
core.pack.dunbrack: Reading Dunbrack Libraries
core.pack.dunbrack: Reading /nas02/home/k/i/kimdn/rosetta/rosetta_database/rotamer/ExtendedOpt1-5/cys.bbdep.rotamers.lib
...
core.pack.dunbrack: Reading /nas02/home/k/i/kimdn/rosetta/rosetta_database/rotamer/ExtendedOpt1-5/asp.bbdep.rotamers.lib
core.pack.dunbrack: Reading /nas02/home/k/i/kimdn/rosetta/rosetta_database/rotamer/ExtendedOpt1-5/asp.bbdep.densities.lib
core.pack.dunbrack: Reading /nas02/home/k/i/kimdn/rosetta/rosetta_database/rotamer/ExtendedOpt1-5/asp.bbind.chi2.Definitions.lib
Creating tricubic splines for the backbone-dependent non-rotameric chi scores
Finished creating tricubic splines
core.pack.dunbrack: Reading /nas02/home/k/i/kimdn/rosetta/rosetta_database/rotamer/ExtendedOpt1-5/glu.bbdep.rotamers.lib
core.pack.dunbrack: Reading /nas02/home/k/i/kimdn/rosetta/rosetta_database/rotamer/ExtendedOpt1-5/glu.bbdep.densities.lib
core.pack.dunbrack: Reading /nas02/home/k/i/kimdn/rosetta/rosetta_database/rotamer/ExtendedOpt1-5/glu.bbind.chi3.Definitions.lib
Creating tricubic splines for the backbone-dependent non-rotameric chi scores
Finished creating tricubic splines
core.pack.dunbrack: Reading /nas02/home/k/i/kimdn/rosetta/rosetta_database/rotamer/ExtendedOpt1-5/phe.bbdep.rotamers.lib
core.pack.dunbrack: Reading /nas02/home/k/i/kimdn/rosetta/rosetta_database/rotamer/ExtendedOpt1-5/phe.bbdep.densities.lib
core.pack.dunbrack: Reading /nas02/home/k/i/kimdn/rosetta/rosetta_database/rotamer/ExtendedOpt1-5/phe.bbind.chi2.Definitions.lib
...
core.pack.dunbrack: Reading /nas02/home/k/i/kimdn/rosetta/rosetta_database/rotamer/ExtendedOpt1-5/asn.bbdep.densities.lib
core.pack.dunbrack: Reading /nas02/home/k/i/kimdn/rosetta/rosetta_database/rotamer/ExtendedOpt1-5/asn.bbind.chi2.Definitions.lib
Creating tricubic splines for the backbone-dependent non-rotameric chi scores
Finished creating tricubic splines
...
core.pack.dunbrack: Dunbrack 2010 library took 35.51 seconds to load from ASCII
core.pack.dunbrack: Memory usage:
core.pack.dunbrack: CYS with 187664 bytes
...
core.pack.dunbrack: TYR with 5789104 bytes
core.pack.dunbrack: Total memory on Dunbrack Libraries: 93727608 bytes.
Warning: Unable to locate database file rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin
Warning: Unable to locate database file rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin
core.pack.dunbrack: Opening file /nas02/home/k/i/kimdn/rosetta/rosetta_database/dun10XtCuTa for output.
protocols.cluster: RESCORING: S_00000345_from_2_1_0001.pdb
protocols.cluster: Adding struc: 2.122e-314
core.pack.task: Packer task: initialize from command line()
protocols.cluster: RESCORING: S_00000345_from_2_1_0002.pdb"
(0000241)
kimdn   
2013-04-02 13:45   
After reading rocco's note, I erased
"rosetta_database/rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin"

and ran cluster again and this time it ran well.

Since 'Dunbrack10.lib.bin_led_seg_fault_compiled_at_54637' is too big, I copy the file into Kuhlman lab's internal site. (@ contador /home/kimdn/scr/data/do_not_erase/Dunbrack10.lib.bin_led_seg_fault_compiled_at_54637)





View Issue Details
237 [Rosetta] Bad Coding minor always 2013-04-01 20:01 2013-04-01 23:15
Labonte All platforms  
Labonte Any  
low Any  
resolved Trunk  
fixed  
none    
none Trunk  
   
any using patch files that remove properties
N/A
54635
ResidueType::delete_property() actuals ADDS duplicate properties to ResidueType
delete_property() was clearly a cut-and-paste modification of add_property() and

properties_.push_back( property );

was left in by accident in l. 1246, such that after setting the corresponding boolean to false, a given property is double-added to the vector1 properties_.
N/A
Select this if your bug report applies to any platform.
Notes
(0000236)
Labonte   
2013-04-01 23:15   
converted push_back() to erase()





View Issue Details
236 [Rosetta] Crash crash always 2013-03-29 19:16 2013-04-01 12:39
amelie All platforms  
amelie Any  
normal Any  
assigned Trunk  
open  
none    
none  
   
all, presumably
rosetta_source/bin/score.macosgccrelease -database rosetta_database/ -ignore_unrecognized_res -s 3itb_clean.pdb
Rosetta crashes on missing atoms in unrecognized SUCK residues
This PDB contains several non-canonical residues. Rosetta doesn't discard them, but then fails to identify them properly, and finally exits with "too many tries in fill_missing_atoms!". This might be because one of the residues has the 3-letter-code SUC, which is close to the internally used SUCK.

protocols.jobdist.JobDistributors: Looking for an available job: 1 1 local_scratch/clean/3itb_clean.pdb 1
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 6400 residue types
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 347 in file local_scratch/clean/3itb_clean.pdb. Best match rsd_type: GLY
core.io.pdb.file_data: [ WARNING ] discarding 23 atoms at position 349 in file local_scratch/clean/3itb_clean.pdb. Best match rsd_type: SUCK
core.io.pdb.file_data: Adding undetected upper terminus type to residue 347
core.io.pdb.file_data: Adding undetected lower terminus type to residue 349
core.conformation.Residue: WARNING: Residue connection id changed when creating a new residue at seqpos 349
core.conformation.Residue: WARNING: ResConnID info stored on residue 350 is now out of date!
core.io.pdb.file_data: Adding undetected upper terminus type to residue 350
core.conformation.Conformation: [ WARNING ] missing heavyatom: ORIG on residue SUCK 348

core.conformation.Conformation: [ WARNING ] missing heavyatom: ORIG on residue SUCK 348
[... very many repeats of the line above ... ]

ERROR: too many tries in fill_missing_atoms!
ERROR:: Exit from: src/core/conformation/Conformation.cc line: 2664
Error: Must call shutdown() when finished using job distributor!
caught exception

[ERROR] EXCN_utility_exit has been thrown from: src/core/conformation/Conformation.cc line: 2664
ERROR: too many tries in fill_missing_atoms!
see command line below
Select this if your bug report applies to any platform.
3itb_clean.pdb (215,434) 2013-03-29 19:16
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=23&type=bug
Notes
(0000230)
smlewis   
2013-04-01 12:39   
SUCK has no business being active by default. Remove it from the default ResidueTypeSet (by #commenting it out in residue_types.txt) and this should go away.





View Issue Details
201 [Rosetta] Bad Coding minor always 2013-03-07 15:43 2013-03-30 16:57
Labonte All platforms  
Labonte Any  
low Any  
assigned Trunk  
open  
none    
none  
   
N/A
N/A
Feature Request
Show() methods are missing for a large number of classes
As discussed at MiniRosettaCON2013, Show() and/or operator<< methods are useful for:
A) Interactive use in PyRosetta
B) Debugging
C) Standardized output

However, many classes have no implementation for Show() or operator<<.

It was proposed that Show() should be added as a virtual or pure virtual method to most objects and that operator<< should be written to call Show().
Select this if your bug report applies to any platform.
Notes
(0000228)
Labonte   
2013-03-29 16:56   
Status Update:
For now, I have simply made show() virtual in Mover and properly implemented operator<< to call it; thus, every Mover will now at least print SOMETHING.

Doing this uprooted several improperly implemented show()s that were not const; I have corrected this in the following Movers/Protocols:
AntibodyModelerProtocol
CDRsMinPackMin
GraftCDRLoopsProtocol
SnugDock
SnugDockProtocol
ThreadingMover
DockingProtocol
TemperedDocking
RemodelGlobalFrame
LoopRefineInnerCycle
LoopRefineInnerCycleContainer
RepackTrial
ShearMinCCDTrial
SmallMinCCDTrial
(0000229)
Labonte   
2013-03-30 16:57   
Status Update:
I modified a large chunk of Movers to have their operator<< methods call their show() method, which I had to write (copying over the gist of the previous operator<< method) in every case. This new show() method calls parent::show(). All the operator<< methods were then "unfriended", as there is no need for them to have access to private data in any of the cases.

The modified Movers are:
    RingConformationMover
    ConformerSwitchMover
    CcdLoopClosureMover
    LoopMover_CCD
    PyMolMover
    5× RigidBodyMovers
    SmallMover
    ShearMover
    ClassicFragmentMover
    MinMover
    PackRotamersMover
    ReturnSidechainMover
    RotamerTrialsMinMover
    RotamerTrialsMover
    SwitchResidueTypeSetMover





View Issue Details
194 [Rosetta] Bad Coding minor always 2013-03-01 12:40 2013-03-29 16:53
smlewis  
Labonte  
normal  
assigned  
open  
none    
none  
   
NA
NA
Mover::fresh_instance() should be pure virtual in base class
Thankless task but it needs doing - bootcamp?
Notes
(0000227)
Labonte   
2013-03-29 16:51   
Status Update:
I am implementing fresh_instnace() (and often, therefore, an empty constructor) for those Movers not having them. Thus far, I have fixed:
SequenceMover
RandomMover
CycleMover
RepeatMover
TrialMover
RNA_FragmentMover
RotamerRecoveryMover
SmallMover
ShearMover
ClassicFragmentMover
MissingDensityToJumpMover
ReturnSidechainMover





View Issue Details
191 [Rosetta] Bad Coding minor always 2013-03-01 12:34 2013-03-29 16:52
smlewis  
Labonte  
low  
assigned  
open  
none    
none  
   
NA
NA
Feature Request
Mover::clone() should be pure virtual in base class
Thankless task but it needs doing - bootcamp?
Notes
(0000226)
Labonte   
2013-03-29 16:49   
Status Update:
I am implementing clone() (and usually, therefore, a copy constructor) for those Movers not having them. Thus far, I have fixed:
SequenceMover
RandomMover
CycleMover
RepeatMover
TrialMover
RNA_FragmentMover
RotamerRecoveryMover
SmallMover
ShearMover
ClassicFragmentMover
MissingDensityToJumpMover
ReturnSidechainMover





View Issue Details
235 [Rosetta] Input Handling minor always 2013-03-28 11:38 2013-03-28 11:38
dimaio  
 
normal  
new  
open  
none    
none  
   
all
na
Feature Request
[Feature request] Support for hybrid36 PDB reading/writing
If a PDB has <100k atoms the format is identical but hybrid36 allows support for large structures in a single file. http://cci.lbl.gov/hybrid_36/ [^]
There are no notes attached to this issue.





View Issue Details
200 [Rosetta] Input Handling minor always 2013-03-07 08:39 2013-03-26 18:42
momeara All platforms  
Any  
normal Any  
new  
open  
none    
none  
   
all
benchmark.linuxclangrelease -asdflkajsdf
Feature Request
When given a bad option on the command line print what is usually displayed with -help
When a bad option is given on the command line, currently it comes back with something like:

ERROR: Option matching -scale_factor not found in command line top-level context
caught exception ERROR: Option matching -scale_factor not found in command line top-level context

Wouldn't it be nice it came back with that error and then (formated in fixed with font of course):


Usage:

../../../bin/benchmark.postgres.linuxclangrelease [options]

Options: [Specify on command line or in @file]

Showing only relevant options...


                        Option | Setting |Type| Description
--------------------------------------------------------------------------------------
                               | | |
                        run: | | |
               benchmark_scale | 1 | R| Amount to scale number of
                               | | | cycles to repeate each
                               | | | test
             run_one_benchmark | | S| Run just a single
                               | | | performance benchmark
               benchmark_scale | 1 | R| Amount to scale number of
                               | | | cycles to repeate each
                               | | | test
             run_one_benchmark | | S| Run just a single
                               | | | performance benchmark
                               | | |
                    in:path: | | |
                      database | | (P)| Database file input search
                               | | | paths. If the database is
                               | | | not found the ROSETTA3_DB
                               | | | environment variable is
                               | | | tried.
Select this if your bug report applies to any platform.
Notes
(0000199)
smlewis   
2013-03-21 09:09   
There are (at least) two types of bad options:

A) Correct but insufficiently specific option (did you mean -packing:repack_only, or -somethingelse:repack_only?)

B) Never-correct options (-this_option_does_not_exist)

We only want to print help for B; for A it already prints a nice message requesting the user disambiguate their choice (and what the unambiguous choices are).





View Issue Details
169 [Rosetta] Bad Coding minor always 2013-01-11 16:19 2013-03-26 16:15
smlewis All platforms  
AndrewLeaverFay Any  
normal Any  
resolved Trunk  
fixed  
none    
none Trunk  
  Trunk  
scons compile time
scons; run:version
Feature Request
54533
Good idea to move svn_version.py to devel?
There is an auto-versioning script which runs every time you do scons. It detects git as well as SVN versions, and allows the -run:version flag to work. It may be a good idea to move the system from core to devel; this means that each-and-every git commit when developing won't cause the core and protocols libraries to re-link. The run:version code would have to move to devel:init, which is no longer a cost because all apps use devel:init now.

Also, I think someone (Rocco?) wrote in a flag to scons to skip running svn_version.py, which is an alternate way to prevent this problem...if that's true can someone mention it on this bug report?
Select this if your bug report applies to any platform.
Notes
(0000138)
rmoretti   
2013-01-11 16:47   
The scons flag to skip the versioning check is --nover.

The other option is to use cmake, which only runs the versioning script in the initial generation phase, but not for any of the rebuild runs.

--

One possible complication to moving the versioning is that currently the core::init tracer does the -run:version printing. I'd be against moving it to the devel:init tracer, as currently the single core:init tracer is printing the relevant info to recapitulate the run (version information, command line, random seed), and spreading that out to other tracers would complicate managing logging.

One way around that is to possibly have static versioning strings at the core level, which the devel level then modifies (prior to calling core::init).

--

Finally, not all applications use devel::init, not even all the ones in public/ - run a grep in the src/apps directory just to see. Some are probably just mistaken, but there's some issues with devel for things like BOINC (though I don't know the exact details). Not a show-stopper, but something to be taken into consideration.
(0000181)
smlewis   
2013-03-16 15:10   
This will be harder to move than we thought: there are dependencies on svn_version; the features / database support in particular does actually use this data. Tim will post a note on ideas to use global mutable data to, um, fix this.

16:08:59 contador ~/git_from_andrew/rosetta/rosetta_source/src> ack-grep -l svn_version
apps/pilot/mike/rosetta_backend.cc
python/bindings/BuildBindings.py
python/bindings/src/__init__.py
protocols/jobdist/JobDistributors.hh
protocols/jobdist/JobDistributors.cc
protocols/features/ProtocolFeatures.cc
protocols/features/BatchFeatures.cc
protocols/jd2/AtomTreeDiffJobOutputter.cc
core/svn_version.cc
core/svn_version.hh
core/init.cc
(0000182)
tjacobs2   
2013-03-16 15:17   
We could simply move svn_version.cc (although we should really change it to git soon) to devel, and allow it to update the same way we do now. Then, at runtime we use a function call in devel init.cc to set a global data member that lives as low as we want based on the const data set by the compilation script.
(0000219)
AndrewLeaverFay   
2013-03-26 16:12   
SVN versioning script now writes the version and url info to devel/svn_version.cc. In devel::init(), this code is handed up to the core library before protocols::init() gets called. Then when core::init() is called, the version has been written.





View Issue Details
233 [Rosetta] Bad Coding minor always 2013-03-26 14:55 2013-03-26 14:55
amelie All platforms  
amelie Any  
normal Any  
assigned Trunk  
open  
none    
none  
   
loopmodel.<binary>
loopmodel.<binary> -kic_rama2b
loopmodel.<binary> with -kic_rama2b needs 5G of memory
The random phi/psi lookup table for using rama2b in next-generation KIC needs lots of memory. Code should be refactored to be more memory efficient.
loopmodel.<binary> -kic_rama2b
Select this if your bug report applies to any platform.
There are no notes attached to this issue.





View Issue Details
227 [Rosetta] Bad Coding minor always 2013-03-22 10:03 2013-03-25 13:12
smlewis  
momeara  
normal  
resolved  
fixed  
none    
none  
   
EXIT_THROWS_EXCEPTION
EXIT_THROWS_EXCEPTION
54502
cleanup removal of EXIT_THROWS_EXCEPTION
Post bug 0000189, we need to remove all the EXIT_THROWS_EXCEPTION mentions in he codebase, since it no longer exists.

I will get the documentation ones, but someone (Matt?) should get the features ones, and someone (?) should get the cmake ones.
rosetta> ack-grep -a EXIT_THROWS_EXCEPTION
rosetta_demos/protocol_capture/2010/AnchoredDesign/raw_documentation/RobustRosetta.dox
33:@li ensure that the preprocessor statement EXIT_THROWS_EXCEPTION is defined. You can do this on command line, or modify user.settings. For example, modify user.settings to include: "appends" : { "defines" : ["EXIT_THROWS_EXCEPTION"], },

rosetta_source/doc/RobustRosetta.dox
33:@li ensure that the preprocessor statement EXIT_THROWS_EXCEPTION is defined. You can do this on command line, or modify user.settings. For example, modify user.settings to include: "appends" : { "defines" : ["EXIT_THROWS_EXCEPTION"], },

rosetta_source/cmake/build_native_client_32/CMakeLists.txt
23:ADD_DEFINITIONS(-DEXIT_THROWS_EXCEPTION)

rosetta_source/cmake/build_backend/CMakeLists.txt
7:ADD_DEFINITIONS(-DEXIT_THROWS_EXCEPTION)

rosetta_source/cmake/build_release_static/CMakeLists.txt
7:ADD_DEFINITIONS(-DEXIT_THROWS_EXCEPTION)

rosetta_source/cmake/build_native_client/CMakeLists.txt
23:ADD_DEFINITIONS(-DEXIT_THROWS_EXCEPTION)

rosetta_source/src/apps/public/interface_design/anchored_design/AnchorFinder.cc
21:// make sure EXIT_THROWS_EXCEPTION is defined in user.settings.

rosetta_source/src/protocols/jd2/JobDistributor.cc
874: std::exit(1); // Using pure exit instead of utility_exit_with_status to avoid recursion when compile with EXIT_THROWS_EXCEPTION

rosetta_source/tools/build/user.settings
31: "defines" : ["EXIT_THROWS_EXCEPTION"],

rosetta_source/tools/build/site.settings.killdevil
31: "defines" : ["EXIT_THROWS_EXCEPTION"],

rosetta_source/tools/build/site.settings.orchestra
51: "defines" : ["EXIT_THROWS_EXCEPTION"],

rosetta_tests/features/sample_sources/top8000_rotamer_recovery_sp2_RTMin/input/REAME.txt
10: "defines" : ["EXIT_THROWS_EXCEPTION"],

rosetta_tests/features/sample_sources/top8000_relax_sp2/input/README.txt
10: "defines" : ["EXIT_THROWS_EXCEPTION"],

rosetta_tests/features/sample_sources/top8000/input/REAME.txt
10: "defines" : ["EXIT_THROWS_EXCEPTION"],

rosetta_tests/features/sample_sources/top8000_sp2/input/REAME.txt
10: "defines" : ["EXIT_THROWS_EXCEPTION"],

rosetta_tests/features/sample_sources/top8000_rotamer_recovery_score12prime_RTMin/input/REAME.txt
10: "defines" : ["EXIT_THROWS_EXCEPTION"],

rosetta_tests/features/sample_sources/top8000_relax/input/REAME.txt
10: "defines" : ["EXIT_THROWS_EXCEPTION"],

rosetta_tests/features/sample_sources/top8000_rotamer_recovery_sp2_MinPack/input/REAME.txt
10: "defines" : ["EXIT_THROWS_EXCEPTION"],

rosetta_tests/features/sample_sources/top8000_rotamer_recovery_score12prime_MinPack/input/REAME.txt
10: "defines" : ["EXIT_THROWS_EXCEPTION"],
Notes
(0000207)
smlewis   
2013-03-22 10:12   
with SVN 54448, I resolved:

    rosetta_demos/protocol_capture/2010/AnchoredDesign/raw_documentation/RobustRosetta.dox
    rosetta_source/doc/RobustRosetta.dox
    rosetta_source/src/apps/public/interface_design/anchored_design/AnchorFinder.cc
    rosetta_source/src/protocols/jd2/JobDistributor.cc
    rosetta_source/tools/build/site.settings.killdevil
    rosetta_source/tools/build/site.settings.orchestra

There is still some question of what the signal handler in JD2 should be doing.
(0000208)
renfrew   
2013-03-22 10:37   
(edited on: 2013-03-22 10:42)
Should rosetta_source/tools/build/user.settings even be tracked by svn/git?

EDIT: Nevermind its not. You just have ETE in yours.

(0000209)
smlewis   
2013-03-22 11:19   
You are correct, it's not tracked by git...that's just the return from ack, which doesn't look at .gitignore.





View Issue Details
215 [Rosetta] Bad Coding minor always 2013-03-16 10:37 2013-03-25 11:01
smlewis  
 
normal  
new Trunk  
open  
none    
none  
   
none, git issue
none, git issue
top-level .gitignore after we move to git
This is a child of bug 0000207 - rosetta_tools had no .gitignore. After we move to git and the directory/repository structure stabilizes, we need a toplevel .gitignore for globally-ignored files, including text editor temp files and python binaries; at minimum:

*.pyc
._*
*~
\#*\#
Notes
(0000218)
smlewis   
2013-03-25 11:01   
Note: SVN 54493 puts one in for rosetta_tests as a temp backstop





View Issue Details
174 [Rosetta] Bad Coding minor always 2013-02-21 08:52 2013-03-25 09:27
smlewis All platforms  
Any  
low Any  
new Trunk  
open  
none    
none  
   
integration tests
N/A
4FXN is a strange (bad?) choice for use in tests
4FXN is used in many integration tests:

9:51:15 somarriba ~/LOCAL/super_pure_dont_change/rosetta_tests/integration> find . -name "*4fxn*" | grep -v ".svn"
./tests/loop_modeling/inputs/4fxn.start_0001.pdb
./tests/loop_modeling/inputs/cc4fxn_03_05.200_v1_3.gz
./tests/loop_modeling/inputs/4fxn.loop_file
./tests/loop_modeling/inputs/cc4fxn_09_05.200_v1_3.gz
./tests/torsion_restricted_sampling/input/4fxn.start.pdb
./tests/torsion_restricted_sampling/input/4fxn.loop
./tests/KIC_refine/input/4fxn.start.pdb
./tests/KIC_refine/input/4fxn.loop
./tests/next_generation_KIC/input/4fxn.start.pdb
./tests/next_generation_KIC/input/4fxn.loop
./tests/kinematic_looprelax/input/4fxn.start.pdb
./tests/kinematic_looprelax/input/4fxn.loop
./tests/rosetta_scripts_loops/4fxn.loop_file
./new/loop_modeling/inputs/4fxn.start_0001.pdb
./new/loop_modeling/inputs/cc4fxn_03_05.200_v1_3.gz
./new/loop_modeling/inputs/4fxn.loop_file
./new/loop_modeling/inputs/cc4fxn_09_05.200_v1_3.gz

but, the PDB says it's obsolete (as of 1997!):

http://pdb.rcsb.org/pdb/explore/obsolete.do?obsoleteId=4FXN [^]

reports:
4FXN was obsoleted on 1997-03-12 and superseded by 2FOX
Select this if your bug report applies to any platform.
Notes
(0000214)
smlewis   
2013-03-25 09:27   
Also, for the loop_modeling itest (that's the CCD test), the first loop chosen (LOOP 54 64 0 0.0 X) is directly adjacent to an FMN that's missing in the input and ignored by Rosetta.





View Issue Details
229 [Rosetta] Bad Coding minor always 2013-03-24 18:58 2013-03-24 19:03
rmoretti  
 
normal  
new Trunk  
open  
none    
none  
   
na
na
protocols::scoring::Interface requires a pre-scored pose.
If you call protocols::scoring::Interface.calculate(pose) on a pose that hasn't been scored yet, you'll get an assertion error in core::scoring::Energies::energy_graph() regarding the bad energy graph state of the pose.

You'll also get the error if you use the Interface object indirectly, for example through the RestrictToInterface task operation.
Aside from causing an assertion error in debug mode, this behavior may introduce a bug/undesired behavior if the state of the pose has changed from the last time it was scored. (e.g. the energy graph might not be up to date).

It looks like the energy graph dependance is solely to look at the pair distance (see Interface::protein_calculate() and symmetric_protein_calculate() ), and probably should be rewritten to avoid depending on the energy graph (as ligand_calculate() is).
Notes
(0000213)
smlewis   
2013-03-24 19:03   
RestrictToInterfaceOperation was written solely to get around this behavior - perhaps a parent bug is "we have a ton of different, mostly-identically-behaving ways to detect interfaces"





View Issue Details
189 [Rosetta] Crash major always 2013-03-01 10:46 2013-03-22 10:03
smlewis  
renfrew  
normal  
resolved  
fixed  
none    
none Trunk  
   
EXIT_THROWS_EXCEPTION, jd2
EXIT_THROWS_EXCEPTION, jd2
54428
Turn on EXIT_THROWS_EXCEPTION by default
MiniCON 2013 defaults change report 3

After bug 0000168 has been fixed (the all-executables-try/catch), we should alter SCons to always #define EXIT_THROWS_EXCEPTION, or equivalently just take the #ifdefs off that code in utility/exit.cc.

This will have the effect of catching all utility_exits as exceptions, some of which can be handled by the job distributor.

This will have the undesired side effect of NOT crashing some code that SHOULD crash - particularly, Movers that are not exception-safe will continue to be used by the JobDistributor on the next job instead of quitting. Perhaps Mover reinitialization should be forced after any exception is caught?
Notes
(0000149)
smlewis   
2013-03-01 10:51   
This is related to robustifying Rosetta against crashes, but not user support (minicon 2013 defaults)
(0000206)
renfrew   
2013-03-21 15:06   
With the resolution of bug 168 This was added at r54428.
https://svn.rosettacommons.org/trac/changeset/54428 [^]





View Issue Details
221 [Rosetta] Crash minor always 2013-03-19 16:58 2013-03-21 15:09
rmoretti  
 
normal  
new Trunk  
open  
none    
none  
   
many
see above
Crashes on blank command line
No programs should segfault or die with inscrutable errors when no flags (or just -database) are passed on the command line. (Actually that last bit should be "ever", but we'll start with "when no flags are passed".)
Quick and *very* dirty way to evaluate these for released applications from within python (in rosetta_source directory):

import os
exec(open("src/apps.src.settings").read())

for k in sources:
  for p in sources[k]:
    print "====", p, "===="
    os.system("./bin/%s.default.linuxgccrelease -database ../rosetta_database -overwrite > /dev/null"%p)

(you'll need to examine the ones that "fail" closely, as some may be exiting with reasonable error messages).
Segmentation Faults (definitely not good) in r54387 :

supercharge
antibody_assemble_CDRs
antibody_model_CDR_H3
fragment_picker
remodel
doug_dock_design_min_mod2_cal_cal
FloppyTail
hbs_design
oop_design
rna_database

There are many others that don't have useful information printed to stderr, though those may have helpful information printed to stdout.
Notes
(0000187)
momeara   
2013-03-19 18:59   
Once these apps have been fixed, can we make this "quick and *very* dirty script" into an integration test that tests all the compiled apps in bin?
(0000188)
smlewis   
2013-03-20 08:59   
I'll take care of FloppyTail.

Is fixing this per-app correct? Is there *any* application that can run with no flags, or with only -database? Should we catch this case at option system read time?
(0000197)
rmoretti   
2013-03-20 22:21   
I'd probably recommend that some time be spent on making the script a little less hacky (better program discovery, better execution launch) and figuring out what to do about the files it litters the directory with, but I don't have a fundamental objection to making it an integration test. The one concern is that the pass/fail evaluation isn't automatic - there's some judgement call involved, especially if you want it do more than just segfault/no segfault testing.

Fixing it per app - specifically, fixing the issue that's causing the segfaults - is certainly something that needs to be done. This particular case is more illustrative of brittleness in handling user input (e.g. what happens if a user forgets a flag, or supplies an empty PDB, etc.), rather than a specific use-case to consider.

Making a no flag run do something else (e.g. print the application help) might be something to consider, but it would be a separate issue from fixing the missing-flag brittleness.
(0000198)
momeara   
2013-03-20 22:51   
There's a thing called "fuzz testing" (http://en.wikipedia.org/wiki/Fuzz_testing [^]) that tries to induce crashes, by providing nonsensical inputs. I can imagine that this would turn up quite a few problems with Rosetta.





View Issue Details
226 [Rosetta] Input Handling minor always 2013-03-21 12:15 2013-03-21 15:08
smlewis  
 
normal  
new  
open  
none    
none  
   
exception handling
exception handling
Feature Request
Feature Request: catch option-system throws locally; handle them somewhat more fancily
Mike Tyka added the feature for the option system to throw exceptions for erroneous options. This feature request is to extend that a bit.

There are (at least) two types of bad options:

A) Correct but insufficiently specific option (did you mean -packing:repack_only, or -somethingelse:repack_only?)

B) Never-correct options (-this_option_does_not_exist)

For exception type A (some exception subclass), print a message of what the other choices are (this code already exists), then re-throw for a potential re-handing at executable level.

For B (different exception class), print whatever -help would print, then re-throw for the executable to handle if it can.

We need to re-throw in all cases because A) our all-executables-catch test depends on catching a badly formatted option and B) the executable may know much more about what options were meant than we do in core::init.
There are no notes attached to this issue.





View Issue Details
168 [Rosetta] Crash crash always 2013-01-04 10:55 2013-03-21 15:08
smlewis All platforms  
mtyka Any  
high Any  
resolved Trunk  
fixed  
none    
none  
   
any
ex: AnchoredDesign -thisisnotanoption
53112
Bad option reads throw uncaught exceptions
I don't know how long this has been going on, but bad option reads (non-existent option files, or non-existent options) causes the option reader to throw uncaught exceptions. The option reading is done inside init, which is NOT expected to be wrapped at app-level in a try/catch. I'm guessing the right place to put the try/catch is at the top of devel::init or protocols::init, on the theory that failed initialization is always a killer (but should be cleanly reported).
fixbb IS wrapped in a try/catch for some reason - is that the new standard?
Select this if your bug report applies to any platform.
Notes
(0000134)
momeara   
2013-01-04 11:03   
(edited on: 2013-01-04 11:06)
Steven, why do you think init() shouldn't be wrapped in an app-level try catch block? Since un caught exceptions fail harder than segfaults, it's worth wrapping all code in any main block in a try catch block in all apps. I've wrapped a few applications but I think all of them should be wrapped.

Adding a catch and re-throw around the various init() calls wouldn't hurt, though, so more information can be added to the error message.

(0000135)
smlewis   
2013-01-04 11:10   
If we want all applications (all our code) to forever be wrapped in try/catch blocks, we can, but it's an unenforceable mandate. Each time someone writes a new one they'll have to remember to add in a bunch of copy/pasted try/catch from some other app to do error handling (duplication). Ideally at application level we should have only init and a call to the job distributor; the latter already has appropriate try/catches so only init needs one.

If we want to put try/catch around all of each application, we can, but it seems...unelegant?
(0000136)
smlewis   
2013-01-04 11:10   
PS, this is also going to rosetta-devel
(0000148)
smlewis   
2013-03-01 10:42   
(edited on: 2013-03-01 10:49)
MiniCON 2013 proposed resolution to this bug: A) add try/catch around all executables, possibly as homework at the bootcamp; B) add try/catch for the option system to core::init. If you fix A without B, or B without A, file a bug for the other one please.

(0000157)
renfrew   
2013-03-04 09:18   
The Bonneau lab is going to add try/catch to all apps in a mini action day this week (2013-03-04)
(0000190)
renfrew   
2013-03-20 10:58   
Relating to Note (0000148), why is B required, if all apps have a catch?
(0000191)
smlewis   
2013-03-20 11:09   
1) because if we expect the option system to throw, catching it as close to the option system as possible (with catch code that knows how to handle the option system) is best

2) because someone is going to make a new app without a try/catch wrapper, and catching in core::init will provide a backstop for some of those errors
(0000192)
smlewis   
2013-03-20 11:32   
Having seen your commit log for https://svn.rosettacommons.org/trac/changeset/54403 [^] , I would suggest maybe having the integration test check for a particular type of error via a core::init catcher, instead of looking for an actual uncaught exception via "Abort trap". Either way, this is a 95% solution! Thanks for taking care of it!
(0000193)
smlewis   
2013-03-20 11:34   
A core::init trap also ties neatly to bug 0000200
(0000194)
renfrew   
2013-03-20 12:03   
Alright, I understand the idea of catching the exception near where it was thrown is elegant and bug 0000200 hints at some useful ways the options system could handle options exceptions:
* if an option cant be found it could do a quick check and see if you misspelled an option and say did mean...
* it could tell you if an option matches multiple things and is therefore ambiguous and you need to precede it with more namespace qualifications
* etc.

To do that it sounds like we would want a new exception class (or possibly several), lets say EXCN_Options. Only the app would know the correct options for it self (if you wanted to do something like bug 0000200) so the options catch in core::init would probably need to re-throw and the app would need to have a special catch for EXCN_Option before the catch for EXCN_Base.

As for (2) we added a new integration test that tests everything in bin (whether or not the new app has its own integration test) by passing a bogus option.
(0000195)
renfrew   
2013-03-20 13:01   
(edited on: 2013-03-20 13:02)
I guess I am confused as to what you mean by having the IT check for different types of exceptions from core::init(). Do you mean having something like below in core::init()

try {
...
catch( utility::excn::EXCN_Msg_Exception const & e ) {
   std::cout << "caught message exception" << std::endl;
} catch( utility::excn::EXCN_BadInput const & e ) {
   std::cout << "caught bad input exception" << std::endl;
} catch( utility::excn::EXCN_RangeError const & e ) {
   std::cout << "caught bad range error exception" << std::endl;
} catch( utility::excn::EXCN_NullPointer const & e ) {
   std::cout << "caught null pointer exception" << std::endl;
}
...

and then having the IT look for "caught message exception", "caught bad input exception", "caught bad range error exception", or "caught null pointer exception"?

I think wrapping core::init() in a try/catch (internally) would only catch throws that happen during core::init().

Do we think that with these changes (all apps being wrapped with try/catch + the new IT) we can close this bug and remove the #ifdef EXIT_THROW_EXCEPTION tags, ( and close bug 0000189)?

We tested r54403 with that flag turned on and saw no problems.

(0000196)
smlewis   
2013-03-20 18:33   
By "I would suggest maybe having the integration test check for a particular type of error via a core::init catcher", what I meant was that the option-system catcher, living inside core::init and catching only option-system throws (and the rare misc. throw that occurs during option time?), would do something slightly fancier than the standard "print the .msg() string", and instead "print that this is a bad option error, then print the .msg() string".

I didn't think it through, though - this won't work with your desired integration test setup unless the core::init catcher re-throws, which is stupid...so I guess for your integration test to work, (unless there is a better way of forcing a throw than a bad option read), we can't add a core::init option catcher.

I guess we could put code in core::init that throws only in the presence of a flag "-always_die", and then run your integration test in the presence of that to see uncaught exceptions, instead of relying on the option system to throw?
(0000200)
smlewis   
2013-03-21 09:20   
Matt points out that the obvious thing to do, to fix bug 200 and keep this new itest working, is to just have a core::init catcher simply re-throw the option. I was vaguely (and incorrectly) under the impression that we disallowed re-throwing.
(0000201)
renfrew   
2013-03-21 10:10   
I think having the options system throw EXCN_Options and catch EXCN_Options (after we make a EXCN_Options class that is) and re-throwing is a good idea.

The catcher in core::init() could be set up to only catch EXCN_Option. Any other exception type would actually bypass that catch passed up until caught at a place that could handle them (with the catch in the app being a catch all). Apps that want to specifically catch the EXCN_Option could do so before they catch the EXCN_Base, and do their own processing since they will know what options work for them. With respect to bug 200, its probably a good idea for the options catch in core::init() to rethrow, regardless of the new IT, so the app can handle it if it wants to.

It might be good policy for catchers (with the exception of the catch in the app) to first modify the message and then rethrow. This way we will avoid lots of double output where the core::ini() options catcher ouputs a message and then rethrows and then the app base catcher outputs the message again.
(0000202)
renfrew   
2013-03-21 10:13   
Although there are definitely cases (like with utility exit) where we have failed, and just want to stop and exit when we catch them.
(0000203)
renfrew   
2013-03-21 11:46   
Also, I just noticed, that there is already a try/catch around core::init() that catches EXCN_Msg_Exception, prints the msg and re-throws.

https://svn.rosettacommons.org/trac/browser/trunk/rosetta/rosetta_source/src/core/init.cc#L1019 [^]

I think this bug can be closed. Perhaps though another bug should be filed, to have the options system throw a specific type of exception that can be caught and handled rather that just rethrown.
(0000204)
smlewis   
2013-03-21 12:02   
Mike Tyka fixed this in 53112 and didn't tell anyone!
(0000205)
smlewis   
2013-03-21 12:18   
(re-resolving after reassignment)





View Issue Details
188 [Rosetta] Bad Coding minor always 2013-03-01 10:38 2013-03-20 22:26
smlewis  
 
normal  
new  
open  
none    
none  
   
obey_ENDMDL
obey_ENDMDL
Change name of -in:file:obey_ENDMDL
MiniCON 2013 defaults reports 2.1

As an addendum to 0000187, we should change the name of obey_ENDMDL to something more indicative of what it does...suggestions?
Notes
(0000156)
rmoretti   
2013-03-01 13:17   
(edited on: 2013-03-20 22:26)
See 0000187 regarding changing the behavior (and thus name) of the flag.






View Issue Details
225 [Rosetta] Crash crash always 2013-03-20 21:05 2013-03-20 22:09
rpache All platforms  
rmoretti Any  
normal Any  
resolved All  
fixed  
none    
none  
   
probably all
score.macosgccrelease -database rosetta_database -s 1ZHZ_liganded_renumbered.pdb -extra_res_fa 1ZHZ_LG.fa.params
54418
Segmentation fault when loading a structure with ligand params file that contains a PROTON CHI line
Rosetta produces a segmentation fault when loading a structure with a small molecule ligand, where the params file contains a PROTON CHI definition line and no other CHI angle definitions.
This can easily be reproduced with the score app.
The crash does not happen, when the ligand params file contains normal CHI angle def lines.
Select this if your bug report applies to any platform.
bug.tar.gz (74,799) 2013-03-20 21:05
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=22&type=bug
There are no notes attached to this issue.





View Issue Details
224 [Rosetta] Bad Coding minor always 2013-03-20 18:24 2013-03-20 18:24
smlewis  
 
low  
new All  
open  
none    
none  
   
constraints
constraints
cst_file and cst_fa_file are StringVector instead of FileVector options
19:23:25 contador ~/scr/rosetta34/rosetta_source/src> grep cst_file basic/options/options_rosetta.py
                Option( 'cst_file', 'StringVector', desc='constraints filename(s) for centoroid. When multiple files are given a *random* one will be picked.' ),
19:23:28 contador ~/scr/rosetta34/rosetta_source/src> grep cst_fa_file basic/options/options_rosetta.py
                Option( 'cst_fa_file', 'StringVector', desc='constraints filename(s) for fullatom. When multiple files are given a *random* one will be picked.' ),

I think this should be FileVector. Notice also the "centoroid". Whether this is a sane behavior or not (as opposed to concatenation) is a different topic.
https://www.rosettacommons.org/node/3232 [^]
There are no notes attached to this issue.





View Issue Details
222 [Rosetta] Input Handling minor always 2013-03-19 17:02 2013-03-20 11:27
jkleman x86  
OS X  
normal 10.7  
new Trunk  
open  
none    
none  
   
Rosetta, PyRosetta
mypose = pose_from_pdb("test31.pdb"); mypose.dump_pdb("test31out.pdb")
Confirmed As Bug
coords in pose sidechain atoms are nan's, no warning to user
If backbone atoms in a pose are co-linear, no warning shows up that warns the user that the side-chain atoms can't be built. Instead, the coordinates are nan.
#reading into pose in PyRosetta
mypose = pose_from_pdb("test31.pdb")

#writing out
mypose.dump_pdb("test31out.pdb")
test31.pdb (325) 2013-03-19 17:02
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=20&type=bug
Notes
(0000189)
smlewis   
2013-03-20 08:59   
This is confirmed with score_jd2 as well.





View Issue Details
223 [Rosetta] Documentation minor always 2013-03-20 09:59 2013-03-20 09:59
smlewis  
 
normal  
new  
open  
none    
none  
   
RosettaScripts
RosettaScripts using XML with TaskAwareMinMover
Are TaskAwareMinMover and TaskAwareSymMinMover deprecated?
Matt's SVN log on https://svn.rosettacommons.org/trac/changeset/51424 [^] SVN 51424 states "Make MinMover and SymMinMover take {bb, chi, bondangle, bondlength}_task_operations, where it restricts the DOF type in the MoveMap to the residues that are packable. This deprecates TaskAwareMinMover and TaskAwareSymMinMover. The motivation for this is that the TaskAware versions were diverging in their functionality from MinMover and SymMinMover, this will simplify the code and usage through RosettaScripts. Testing in an integration test is coming next. No test failures are expected."

Are TAMinMover and TASMinMover deprecated for general use or only for RosettaScripts? If the former, they need to be removed from code; if the latter, I guess it needs to be removed from the documentation and have its parse_my_tag set to utility_exit?
There are no notes attached to this issue.





View Issue Details
111 [Rosetta] Input Handling minor always 2012-09-27 08:53 2013-03-20 09:59
momeara All platforms  
smlewis Any  
normal Any  
assigned  
open  
none    
none  
   
rosetta_scripts
-
Confirmed As Bug
TaskAwareMinMover and TaskAwareSymMinMover handle tasks differently
TaskAwareMinMover only sets backbone to be free for residues that are designable, while TaskAwareSymMinMover will set the backbone to be free for residues that are packable.

This is probably Neil King's fault but he hasn't signed up for the bug tracker. Bad Neil!
Select this if your bug report applies to any platform.
There are no notes attached to this issue.





View Issue Details
218 [Rosetta] Crash minor always 2013-03-16 11:27 2013-03-19 17:02
kdrew x86  
rmoretti OS X  
normal 10.6  
resolved  
fixed  
none    
none Trunk  
   
relax
./bin/relax.macosgccrelease -database ../rosetta_database/
54387
Seg fault in relax
The relax application segfaults when only the database option is set.
Run:

./bin/relax.macosgccrelease -database ../rosetta_database/
Output:
-snip-
fry2:rosetta_source kdrew$ ./bin/relax.macosgccrelease -database ../rosetta_database/
core.init: Mini-Rosetta version d986849300e5772557ea07c7b76044e93e0f8ddf from git@markula.bio.nyu.edu:rosetta-bonneaulab.git
core.init: command: ./bin/relax.macosgccrelease -database ../rosetta_database/
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-1416404664 seed_offset=0 real_seed=-1416404664
core.init.random: RandomGenerator:init: Normal mode, seed=-1416404664 RG_type=mt19937
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
basic.io.database: Database file opened: scoring/score_functions/MembranePotential/CEN6_mem_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/MembranePotential/CEN10_mem_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/MembranePotential/memcbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/MembranePotential/mem_pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp
basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4
protocols.relax.FastRelax: ================== Using default script ==================
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
Segmentation fault
-snip-
Notes
(0000180)
smlewis   
2013-03-16 12:47   
confirmed on linuxclangrelease
(0000186)
rmoretti   
2013-03-18 19:15   
It looks like there's two issues involved here.

The first is that Conformation::is_residue_typeset() assumes that the conformation that it's being called upon has at least one residue in it. -- The algorithm for Conformation::is_residue_typeset() is somewhat broken to begin with (it arbitrarily picks two residues in the pose and assumes that their residue type sets are representative of the entire pose).

The other issue is that jd2 looks to be feeding an empty pose to the mover in the case where there's no input flags on the command line. Is this behavior the desired one? I notice there's a default for GenericJobInputter if no other input type is specified, with the comment that it's used for abinitio and the like.





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214 [Rosetta] Crash crash always 2013-03-14 10:00 2013-03-18 14:27
duranam  
AndrewLeaverFay  
high  
assigned Trunk  
open  
none    
none  
   
SymPackRotamersMover in RosettaScripts
rosetta_scripts.default.linuxgccdebug @symm_fixbb.flags -parser:protocol symm_fixbb_rrf.xml
SymPackRotamersMover dies with TaskOperation ReadResfile
I am setting up symmetry and using the SymPackRotamersMover to design a membrane protein by only allowing certain amino acids to be designed in at each position as specified by the resfile. However, I found that this error happens with PIKAA as well as with NATAA, but not with NATRO or ALLAA. So it seems to be able to read the resfile, it just doesn't like being told which set of rotamers to choose from?

The example I provided below is with PIKAA and gives the same error I see with NATAA:

src/utility/vectorL.hh:363: utility::vectorL<<anonymous>, T, A>::reference utility::vectorL<<anonymous>, T, A>::operator[](utility::vectorL<<anonymous>, T, A>::index_type) [with long int L = 1l; T = int; A = std::allocator<int>; utility::vectorL<<anonymous>, T, A>::reference = int&; utility::vectorL<<anonymous>, T, A>::index_type = long unsigned int]: Assertion `static_cast< size_type >( i - l_ ) < super::size()' failed.
Got some signal... It is:6
Process was aborted!
The example below contains the all of the flags, xml, span, res etc files needed (and is for a resfile with PIKAA) so..
rosetta_scripts.default.linuxgccdebug @symm_fixbb.flags -parser:protocol symm_fixbb_rrf.xml
report_bug_sympacrot.tar.gz (81,008) 2013-03-14 10:00
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=19&type=bug
Notes
(0000183)
duranam   
2013-03-16 23:07   
When backtracing, it seems it stops here:

in core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers (this=0x224f8320, rotamers=...)
    at src/core/pack/interaction_graph/SymmOnTheFlyInteractionGraph.cc:100

This line reads "state_offset_for_restype_group_[ ii ] = rotamers->get_residue_type_begin( ii ) - 1;





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220 [Rosetta] Incorrect Results major always 2013-03-18 01:40 2013-03-18 02:39
Labonte All platforms  
Labonte Any  
high Any  
resolved Trunk  
fixed  
none    
none Trunk  
   
unknown
unknown
54328
KofNConstraint::calculate_total_cst_score has been returning the wrong total score
While cleaning out warnings, I found the following bug in rosetta_source/src/core/scoring/constraints/KofNConstraint.cc, l. 173:

KofNConstraint::calculate_total_cst_score( EnergyMap const & weights, EnergyMap & emap ) const
{
    core::Real total_score =
            emap[constant_constraint] * weights[constant_constraint] +
            emap[coordinate_constraint] * weights[coordinate_constraint] +
            emap[atom_pair_constraint] * weights[atom_pair_constraint] +
            emap[angle_constraint] * weights[angle_constraint] +
            emap[dihedral_constraint] * weights[dihedral_constraint] +
            emap[backbone_stub_constraint] * weights[backbone_stub_constraint];
            emap[backbone_stub_linear_constraint] * weights[backbone_stub_linear_constraint];

    return total_score;
}

Note that the penultimate emap line has a semicolon where it should have a + sign.
I'll fix this along with my next warnings check in.
Select this if your bug report applies to any platform.
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219 [Rosetta] Bad Coding major always 2013-03-17 00:21 2013-03-17 19:33
Labonte All platforms  
dimaio Any  
high Any  
resolved Trunk  
fixed  
none    
none Trunk  
   
any using cartesian bonding
N/A
54322
negative values assigned to Size in CartesianBondedEnergy.cc
l. 1329:
if (i==1) { atm1="C"; atm2="N"; rt1 = -rsd_type.lower_connect_id(); rt2 = rsd_type.atom_index(" N ");}

l. 1350 also looks fishy to me.
N/A
Is this why the CartesianBondedEnergyBBDepTests unit test is failing?

Also, whoever wrote this needs to add themselves as author with the @author Doxygen tag at the top of the file.
Select this if your bug report applies to any platform.
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110 [Rosetta] Incorrect Results minor always 2012-09-27 08:49 2013-03-16 11:27
momeara All platforms  
Any  
normal Any  
new All  
open  
none    
none  
   
all
-
Confirmed As Bug
bad chain ID in pdb output for large number of chains
With enough chains Rosetta will generate " and ' chains,
instead of what is described in the pdb standard:

http://www.wwpdb.org/procedure.html#toc_4 [^]
Select this if your bug report applies to any platform.
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209 [Rosetta] Bad Coding minor always 2013-03-13 12:17 2013-03-16 10:57
smlewis  
smlewis  
normal  
resolved  
fixed  
none    
none  
   
N/A
N/A
54313
temp files committed to trunk
I expect this will be an unresolveable bug in the permanent sense, but here's a list of the current offenders (plus a git command line to find them):

13:12:36 contador ~/git_from_andrew/rosetta> find . -name "*~" -exec git ls-files {} --error-unmatch \;
rosetta_demos/public/predict_eglinC_ddgs/input_files/mutations.multiples.txt~
rosetta_demos/public/electron_density_molecular_replacement/FOR_AUTHORS.dox~
rosetta_tests/integration/tests/features/parser_script.xml~
rosetta_tests/features/scripts/analysis/plots/secondary_structure/alpha_helices.R~
rosetta_tests/features/scripts/analysis/plots/secondary_structure/pi_helices.R~


13:13:57 contador ~/git_from_andrew/rosetta> find . -name "#*#" -exec git ls-files {} --error-unmatch \;
rosetta_demos/public/predict_eglinC_ddgs/#mutations.txt#
Notes
(0000167)
rmoretti   
2013-03-13 12:59   
Patterns can be put into a .gitignore in the top-level directory. That won't change those already committed, but should reduce future commits.
(0000168)
smlewis   
2013-03-13 13:02   
I think all of these are covered by the existing exclusions, actually - it's just that they were manually added anyway at some point...





View Issue Details
207 [Rosetta] Bad Coding minor always 2013-03-13 11:54 2013-03-16 10:37
smlewis  
smlewis  
none  
resolved  
fixed  
none    
none  
   
SVN / git issue
SVN / git issue
Confirmed As Bug
54253
ERRASER leaves un-ignored .pyc files
rosetta> git status
# On branch master
# Untracked files:
# (use "git add <file>..." to include in what will be committed)
#
# rosetta_tools/ERRASER/erraser_option.pyc
# rosetta_tools/ERRASER/erraser_util.pyc
# rosetta_tools/ERRASER/erraser_wrapper.pyc
# rosetta_tools/ERRASER/measure_params.pyc
nothing added to commit but untracked files present (use "git add" to track)
Notes
(0000165)
smlewis   
2013-03-13 12:07   
rosetta_tools had no .gitignore...fixed in my local git but this needs to be crosschecked against svn
(0000166)
rmoretti   
2013-03-13 12:56   
This somewhat raises the question of where .gitignore should be located. Right now it's in rosetta_source (with a few extra ones scattered around). Should that be moved up one directory to rosetta/ proper to apply to all the directories?

This would not only fix the .pyc issues, but would also apply to text editor temporary/backup files and Mac-like shell resouce files (.DStore, etc.) in the non-source directory.
(0000169)
smlewis   
2013-03-13 13:04   
I think a toplevel .gitignore is appropriate in the long term, but it should probably wait until after we move the whole community to git - I think ultimately one will cover source/database/tests, and a separate one each for demos and tools (given my understanding of the git split plan)
(0000176)
smlewis   
2013-03-16 10:32   
I will file a separate child bug for the general case




View Issue Details
206 [Rosetta] Bad Coding minor always 2013-03-13 11:51 2013-03-16 10:31
smlewis  
smlewis  
normal  
resolved  
fixed