sokrypton / sokrypton/ColabFold

unable to use custom .pdb files as hoped for template

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Description

Expected Behavior

hopefully being able to use a .pdb with some small modifications

Current Behavior

I removed the chains of a complex of my protein (the only crystal structure we have right now is the protein in complexes) pdb ID 4nzr. After removing the deleting the extraneous chains in Chimera then exporting/saving as .pdb it was unable to be used as a .pdb.

Steps to Reproduce (for bugs)

described in current behavior

Please make sure to reproduce the issue after a "Factory Reset" in Colab.
If running locally ypdate you local installation colabfold_batch to the newest version.
Please provide your input if you can share it.
input for the sequence is :

TNLVNQSGYALVASGRSGNLGFKLFSTQSPSAEVKLKSLSLNDGSYQSEIDLSGGANFREKFRNFANELSEAITNSPKGLDRPVPKTEISGLIKTGDNFITPSFKAGYYDHVASDGSLLSYYQSTEYFNNRVLMPILQTTNGTLMANNRGYDDVFRQVPSFSGWSNTKATTVSTSNNLTYDKWTYFAAKGSPLYDSYPNHFFEDVKTLAIDAKDISALKTTIDSEKPTYLIIRGLSGNGSQLNELQLPESVKKVSLYGDYTGVNVAKQIFANVVELEFYSTSKANSFGFNPLVLGSKTNVIYDLFASKPFTHIDLTQVTLQNSDNSAIDANKLKQAVGDIYNYRRFERQFQGYFAGGYIDKYLVKNVNTNKDSDDDLVYRSLKELNLHLEEAYREGDNTYYRVNENYYPGASIYENERASRDSEFQNEILKRAEQNGVTFDENIKRITASGKYSVQFQKLENDTDSSLERMTKAVEGLVTVIGEEKFETVDITGVSSDTNEVKSLAKELKTNALGVKLKL

ColabFold Output (for bugs)

Please make sure to also post the complete ColabFold output. You can use gist.github.com for large output.

2022-08-01 18:41:52,309 Found 7 citations for tools or databases

ValueError Traceback (most recent call last)
in ()
52 stop_at_score=float(100),
53 prediction_callback=prediction_callback,
---> 54 dpi=dpi
55 )

1 frames
/usr/local/lib/python3.7/dist-packages/colabfold/batch.py in mk_hhsearch_db(template_dir)
249 if res.id[2] != " ":
250 raise ValueError(
--> 251 f"PDB contains an insertion code at chain {chain.id} and residue "
252 f"index {res.id[1]}. These are not supported."
253 )

ValueError: PDB contains an insertion code at chain H and residue index 31. These are not supported.

Context

Providing context helps us come up with a solution and improve our documentation for the future.

Your Environment

Include as many relevant details about the environment you experienced the bug in.

  • Git commit used
  • If you run it on a local system. Please add the server specifications
  • Operating system and version:
    this is being run
    pdb files used.zip
    on google colab

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 colabfold/batch.py and the mk_hhsearch_db entry point, then reproduce the reported failure in Google Colab using the supplied PDB archive and the 4nzr-derived file. Done means the expected behavior for custom PDB templates containing insertion codes is implemented and verified against this workflow.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook, python
Domain
bioinformatics
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
30/100

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