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| ID | Project | Category | View Status | Date Submitted | Last Update | ||||
| 0000021 | Rosetta | [All Projects] Incorrect Results | public | 2012-06-24 15:13 | 2012-08-22 11:21 | ||||
| Reporter | smlewis | ||||||||
| Assigned To | smlewis | ||||||||
| Priority | low | Severity | minor | Reproducibility | sometimes | ||||
| Status | resolved | Resolution | fixed | ||||||
| Platform | All platforms | OS | Any | OS Version | Any | ||||
| Product Version | 3.4 | ||||||||
| Fixed in Version | |||||||||
| Summary | 0000021: UBQ_E2_thioester two ubiquitins mode second lysine drifts | ||||||||
| Description | In UBQ_E2_thioester's experimental two ubiquitins mode, the attacking lysine of the second ubiquitin drifts. The fold tree sets it up so that NZ is colinear with the carbonyl bond is attacking, but when the code runs, that lysine drifts away from its chemically relevant position. I suspect the bug is that the lysine is unintentionally automatically allowed to pack in PackRotamersMover or RotamerTrials, which ignores the fold tree and doesn't refold the upstream ubiquitin through the sidechain (which SidechainMover does, or at least once did and still should). | ||||||||
| Tags | No tags attached. | ||||||||
| Application(s) Affected | UBQ_E2_thioester | ||||||||
| Command Line Used | UBQ_E2_thioester -etc etc etc -two_ubiquitins | ||||||||
| Developer Options | |||||||||
| Fixed in SVN Version | 50679 | ||||||||
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(0000039) smlewis (Administrator) 2012-07-31 14:06 |
The correct fix is almost certainly an extra forbidden residue added to the PreventRepacking operation: //task_factory_->push_back( new protocols::toolbox::task_operations::RestrictToInterfaceOperation ); task_factory_->push_back( new IncludeCurrent ); //prevent repacking at linkage cysteine! PreventRepackingOP prevent(new PreventRepacking); prevent->include_residue(E2_cys); -----> prevent->include_residue(whatever_The_lysine_number_is); task_factory_->push_back(prevent); |
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(0000050) hajosep (Attentive Developer) 2012-08-07 15:43 |
revision 50263 is a partial fix, but is still incomplete. Bug under construction. |
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(0000066) smlewis (Administrator) 2012-08-19 10:38 |
Here's another attempt for a fix: diff --git a/rosetta_source/src/apps/public/scenarios/chemically_conjugated_docking/UBQ_E2_thioester.cc b/rosetta_source/src/apps/public/scenarios/chemically_conjugated_docking/UBQ_E2_thioester.cc index b960de8..cbee2b2 100644 --- a/rosetta_source/src/apps/public/scenarios/chemically_conjugated_docking/UBQ_E2_thioester.cc +++ b/rosetta_source/src/apps/public/scenarios/chemically_conjugated_docking/UBQ_E2_thioester.cc @@ -655,6 +655,7 @@ public: protocols::simple_moves::sidechain_moves::SidechainMoverOP SCmover( new protocols::simple_moves::sidechain_moves::SidechainMover() ); SCmover->set_task(task); SCmover->set_prob_uniform(0); //we want only Dunbrack rotamers, 0 percent chance of uniform sampling + SCmover->set_change_chi_without_replacing_residue(true); backbone_mover->add_mover(SCmover, 1); It can't be checked in at this time due to the relevant code being broken in trunk; someone broke it in retaliation for it failing the headers-only-compile build. |
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(0000077) smlewis (Administrator) 2012-08-21 14:37 |
Revision 50679 is another attempted fix; I am leaving the bug open pending confirmation from Joe |
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Issue History |
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| Date Modified | Username | Field | Change |
| 2012-06-24 15:13 | smlewis | New Issue | |
| 2012-06-24 15:13 | smlewis | Status | new => assigned |
| 2012-06-24 15:13 | smlewis | Assigned To | => smlewis |
| 2012-06-24 15:13 | smlewis | Status | assigned => confirmed |
| 2012-06-24 15:13 | smlewis | Status | confirmed => assigned |
| 2012-07-31 14:06 | smlewis | Note Added: 0000039 | |
| 2012-07-31 14:07 | smlewis | Assigned To | smlewis => hajosep |
| 2012-08-07 15:43 | hajosep | Note Added: 0000050 | |
| 2012-08-19 10:38 | smlewis | Note Added: 0000066 | |
| 2012-08-21 14:37 | smlewis | Note Added: 0000077 | |
| 2012-08-22 11:21 | smlewis | Fixed in SVN Version | => 50679 |
| 2012-08-22 11:21 | smlewis | Status | assigned => resolved |
| 2012-08-22 11:21 | smlewis | Resolution | open => fixed |
| 2012-08-22 11:21 | smlewis | Assigned To | hajosep => smlewis |
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Issue History |
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