MantisBT - Rosetta |
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| ID | Project | Category | View Status | Date Submitted | Last Update |
| 0000129 | Rosetta | [All Projects] Bad Coding | public | 2012-10-09 22:34 | 2012-10-09 22:54 |
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| Reporter | amelie | |
| Assigned To | kylebarlow | |
| Priority | normal | Severity | minor | Reproducibility | always |
| Status | assigned | Resolution | open | |
| Platform | All platforms | OS | Any | OS Version | Any |
| Product Version | All | |
| Fixed in Version | | |
| Application(s) Affected | loopmodel |
| Command Line Used | bin/loopmodel.macosgccrelease -d ~/rosetta_database -s start.pdb -loops:loop_file multiple.loops |
| Developer Options | |
| Fixed in SVN Version | |
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| Summary | 0000129: centroid-stage modeling of multiple loops proceeds one-by-one instead of iteratively |
| Description | When multiple loops are remodeled, in IndependentLoopMover.cc they are built one by one, in their internal order. In contrast, in the refinement protocols, a loop is randomly selected in each iteration. For loops that are close enough to affect each other's position, the current setup is inefficient if a loop that would need to move out of the way is handled after the others -- in this scenario, it's basically not possible to get a good solution out of the perturb/loop building stage. |
| Steps To Reproduce | see IndependentLoopMover.cc |
| Additional Information | consider modifying the LoopMover base class instead of just IndependentLoopMover |
| Tags | No tags attached. |
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| Issue History |
| Date Modified | Username | Field | Change |
| 2012-10-09 22:34 | amelie | New Issue | |
| 2012-10-09 22:34 | amelie | Status | new => assigned |
| 2012-10-09 22:34 | amelie | Assigned To | => kylebarlow |