MantisBT - Rosetta
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IDProjectCategoryView StatusDate SubmittedLast Update
0000309Rosetta[All Projects] Bad Codingpublic2013-10-25 13:222014-01-21 14:04
ReporterLabonte 
Assigned To 
PrioritylowSeverityminorReproducibilityalways
StatusnewResolutionopen 
PlatformAll platformsOSAnyOS VersionAny
Product VersionTrunk 
Fixed in Version 
Application(s) Affectedunknown
Command Line Used-out:levels core.chemical.PatchOperations.hh:400
Developer Options
Fixed in SVN Version
Summary0000309: Patch system fails to patch HIS_D properly in 4 cases
DescriptionWhen 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.
Steps To ReproduceUse the -out:levels core.chemical.PatchOperations.hh:400 flag.
Additional InformationTracer 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
TagsNo tags attached.
Relationships
related to 0000320resolved Labonte Patch system fails to patch SER properly in 158 cases 
Attached Files
Issue History
Date ModifiedUsernameFieldChange
2013-10-25 13:22LabonteNew Issue
2013-10-25 14:06rmorettiNote Added: 0000318
2013-10-25 14:34LabonteDescription Updatedbug_revision_view_page.php?rev_id=97#r97
2013-10-25 14:35LabonteProjectPyRosetta => Rosetta
2013-10-25 14:35LabonteDescription Updatedbug_revision_view_page.php?rev_id=98#r98
2013-10-28 19:25SergeyNote Added: 0000319
2014-01-21 14:04LabonteRelationship addedrelated to 0000320

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)