RosettaCommons / RosettaCommons/PyRosetta.notebooks

Problem with lowres docking script hanging after a couple of decoys

Open
#116 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Jupyter Notebook
Stars
709
Forks
173
Avg merge
5m
Merged PRs (30d)
2

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.

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

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.

Written by the indexing model from the issue text.

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

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.