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IDProjectCategoryView StatusDate SubmittedLast Update
0000042Rosetta[All Projects] Incorrect Resultspublic2012-07-16 14:322012-09-04 19:33
Reportersmlewis 
Assigned To 
PrioritynormalSeverityminorReproducibilityalways
StatusconfirmedResolutionopen 
PlatformOSOS Version
Product VersionAll 
Fixed in Version 
Summary0000042: optH code can increase score
Descriptionhttp://www.rosettacommons.org/content/opth-flag-makes-hydrogen-bond-energy-scores-worse [^]

The attached PDB provides a case where the score with -no_optH true < -no_optH false. This is true mostly due to the hydrogen bonding terms getting worse when optH is active (-no_optH false).
Steps To ReproduceRun PDB through scoring with/without optH. Tested in 3.4 and SVN 49568.
Additional InformationHere are the scores, clipped to the relevant terms:

    score fa_rep fa_intra_rep hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc
no_optH_false -911.639 129.438 2.818 -43.866 -235.198 -69.964 -49.162
no_optH_true -916.848 129.59 2.831 -43.866 -235.198 -73.02 -51.481
Tagshydrogen, scoring
Application(s) Affectedall
Command Line Usedscore_jd2.linuxgccrelease -database rosetta_database -s test.pdb -no_optH [true/false]
Developer Options
Fixed in SVN Version
Attached Files? file icon test.pdb [^] (428,268 bytes) 2012-07-16 14:32
? file icon optH_false_log [^] (16,918 bytes) 2012-07-16 14:39 [Show Content]

- Relationships

-  Notes
(0000028)
smlewis (Administrator)
2012-07-16 14:35

 confirmed for trunk; user reports 3.4 vulnerable as well; unclear if it's a property of this input structure or a general problem
(0000079)
smlewis (Administrator)
2012-08-21 20:06

 The official ruling was "well, packing is stochastic and occasionally packing fails to find a better conformation". Packing isn't guaranteed to lower energy if it can't recover off-rotamer atom placements by using only its database rotamers.

I think we should tweak optH to at least check if the energy is increasing and refuse to return the newly worse-packed sidechains, but as it stands it's considered not a bug but just an insufficiency of Monte Carlo & rotameric sidechains. I'm leaving the bug open in case someone wants to tweak that implementation detail...

- Issue History
Date Modified Username Field Change
2012-07-16 14:32 smlewis New Issue
2012-07-16 14:32 smlewis File Added: test.pdb
2012-07-16 14:35 smlewis Command Line Used ~/LOCAL/super_pure_dont_change/bin/score_jd2.linuxgccrelease -database ~/LOCAL/super_pure_dont_change/rosetta_database/ -s test.pdb -no_optH [true/false] => score_jd2.linuxgccrelease -database rosetta_database -s test.pdb -no_optH [true/false]
2012-07-16 14:35 smlewis Note Added: 0000028
2012-07-16 14:35 smlewis Assigned To => smlewis
2012-07-16 14:35 smlewis Status new => confirmed
2012-07-16 14:39 smlewis File Added: optH_false_log
2012-08-21 20:05 smlewis Assigned To smlewis =>
2012-08-21 20:06 smlewis Note Added: 0000079
2012-09-04 19:33 Labonte Tag Attached: hydrogen
2012-09-04 19:33 Labonte Tag Attached: scoring

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