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IDProjectCategoryView StatusDate SubmittedLast Update
0000021Rosetta[All Projects] Incorrect Resultspublic2012-06-24 15:132012-08-22 11:21
Assigned Tosmlewis 
PlatformAll platformsOSAnyOS VersionAny
Product Version3.4 
Fixed in Version 
Summary0000021: UBQ_E2_thioester two ubiquitins mode second lysine drifts
DescriptionIn 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).
TagsNo tags attached.
Application(s) AffectedUBQ_E2_thioester
Command Line UsedUBQ_E2_thioester -etc etc etc -two_ubiquitins
Developer Options
Fixed in SVN Version50679
Attached Files

- Relationships

-  Notes
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(whatever_The_lysine_number_is);
hajosep (Attentive Developer)
2012-08-07 15:43

revision 50263 is a partial fix, but is still incomplete. Bug under construction.
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/ b/rosetta_source/src/apps/public/scenarios/chemically_conjugated_docking/
index b960de8..cbee2b2 100644
--- a/rosetta_source/src/apps/public/scenarios/chemically_conjugated_docking/
+++ b/rosetta_source/src/apps/public/scenarios/chemically_conjugated_docking/
@@ -655,6 +655,7 @@ public:
             protocols::simple_moves::sidechain_moves::SidechainMoverOP SCmover( new protocols::simple_moves::sidechain_moves::SidechainMover() );
             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.
smlewis (Administrator)
2012-08-21 14:37

Revision 50679 is another attempted fix; I am leaving the bug open pending confirmation from Joe

- Issue History
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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