RosettaCommons / RosettaCommons/foundry

[BUG]

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bug
Dominant language
Python
Stars
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Forks
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Avg merge
4d 4h
Merged PRs (30d)
2

Description

Describe the bug
When I want to introduce symmetry module into my json file, there are always some problems. I noticed that the hotspot and symmetry are in conflict. So I want to ask whether the parameters like select_exposed or buried and unindexed are in the range of hotspots.

To Reproduce
Please describe any:

  • prepare the json file and pdb file, submit the files to predict
  • system architectures (if relevant)
  • structure files - if it refers to output file, there is a photo shown below.
  • input file : a motif combined with dummy ligand and small molecule.
  • errors:JSONDecodeError: Expecting property name enclosed in double quotes: line 19
    column 9 (char 529)
    Expected behavior
    I will get protein structures with desired symmetry and ideal pocket to bury the small molecule.
    Screenshots
    I don't get valid output under symmetric condition.
    But the following graph shows that the generated protein has a large percentage of disordered secondary structures.
Image

Additional context
json file:

symmetry.json.txt

err file:

869663.txt

Contributor guide

Open the contributing guide

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

Start with the attached symmetry.json.txt and 869663.txt files, checking the JSONDecodeError at line 19, column 9 and how the hotspot and symmetry parameters interact. Compare the requested symmetry and buried-pocket settings with the generated structure; done means the configuration parses and produces valid symmetric output with the intended pocket rather than the reported disordered result.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Quiet
Clarity
Needs clarification
Newbie friendliness
25/100

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