RosettaCommons / RosettaCommons/PyRosetta.notebooks
Problem with lowres docking script hanging after a couple of decoys
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Description
I am following the tutorial files in VSCode, and I got to the part of "7.2: Docking Moves in Rosetta" where the following code is executed:
jd = PyJobDistributor("output", 100, scorefxn_low)
while not jd.job_complete:
cen_pose.assign(starting_cen_pose)
dock_lowres.apply(cen_pose)
jd.output_decoy(cen_pose)
This results in a couple of decoys being processed and output as .pdb files, and then the cell keeps running (not frozen), but no more decoys are output. Is this an issue with how much horsepower I have locally, or something else? I have followed the 7.2 tutorial exactly up to that point, and the version of the loop with 10 decoys was able to run to completion. Thanks in advance for any advice.
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
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Research direction
Begin with the tutorial files for section 7.2, “Docking Moves in Rosetta,” and reproduce the PyJobDistributor loop in VSCode. Compare the completed 10-decoy run with the 100-decoy run and inspect which decoys are written as .pdb files. Done means determining why processing stops after a couple of decoys and documenting the required correction or whether the behavior is expected.
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Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100