MantisBT - Rosetta | |||||
View Issue Details | |||||
ID | Project | Category | View Status | Date Submitted | Last Update |
0000236 | Rosetta | [All Projects] Crash | public | 2013-03-29 19:16 | 2013-04-01 12:39 |
Reporter | amelie | ||||
Assigned To | amelie | ||||
Priority | normal | Severity | crash | Reproducibility | always |
Status | assigned | Resolution | open | ||
Platform | All platforms | OS | Any | OS Version | Any |
Product Version | Trunk | ||||
Fixed in Version | |||||
Application(s) Affected | all, presumably | ||||
Command Line Used | rosetta_source/bin/score.macosgccrelease -database rosetta_database/ -ignore_unrecognized_res -s 3itb_clean.pdb | ||||
Developer Options | |||||
Fixed in SVN Version | |||||
Summary | 0000236: Rosetta crashes on missing atoms in unrecognized SUCK residues | ||||
Description | 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creating a new residue at seqpos 349 core.conformation.Residue: WARNING: ResConnID info stored on residue 350 is now out of date!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! | ||||
Steps To Reproduce | see command line below | ||||
Additional Information | |||||
Tags | No tags attached. | ||||
Relationships | |||||
Attached Files | ![]() https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=23&type=bug | ||||
Issue History | |||||
Date Modified | Username | Field | Change | ||
2013-03-29 19:16 | amelie | New Issue | |||
2013-03-29 19:16 | amelie | File Added: 3itb_clean.pdb | |||
2013-04-01 12:39 | smlewis | Note Added: 0000230 | |||
2013-04-01 12:39 | smlewis | Assigned To | => amelie | ||
2013-04-01 12:39 | smlewis | Status | new => assigned |
Notes | |||||
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