sokrypton / sokrypton/ColabFold

Using "trim_inverse" to specific epitope in Antigen for complex building, errored out.

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Description

Expected Behavior

AlphaFold2_advanced.ipynb
A:B:C = VH:VL:Antigen = 1:1:1
trim_inverse(checked), trim:A1-A(#end),B1-B(#end),C(#x)-C(#y)
(#end)=last residue number; C(#x)-C(#y)=specified epitope in Antigen
##The purpose is to narrow down the complex binding surface to epitope region.

Current Behavior

##errored. program stopped. no results. error message below:

KeyError Traceback (most recent call last)
<ipython-input--***********> in ()
11 #@markdown - qid minimum sequence identity with query (%)
12
---> 13 mod_I = cf_af.prep_filter(I, trim, trim_inverse, cov, qid)
14
15 if I["msas"] != mod_I["msas"]:

1 frames
/content/colabfold_alphafold.py in prep_filter(I, trim, trim_inverse, cov, qid, verbose)
504 if trim != "":
505 mod_I.update(trim_inputs(trim, mod_I["msas"], mod_I["deletion_matrices"],
--> 506 mod_I["ori_sequence"], inverse=trim_inverse))
507
508 mod_I["homooligomers"] = [mod_I["homooligomers"][c] for c in mod_I["chains"]]

/content/colabfold_alphafold.py in trim_inputs(trim, msas, deletion_matrices, ori_seq, inverse)
407 trim_idx_i = trim_idx_j = global_idx
408 if i != "" and i[0] in ascii_uppercase:
--> 409 trim_idx_i,i = chain_idx[i[0]], i[1:]
410 if j != "" and j[0] in ascii_uppercase:
411 trim_idx_j,j = chain_idx[j[0]], j[1:]

KeyError: 'T'

Steps to Reproduce (for bugs)

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.

ColabFold Output (for bugs)

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

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
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  • Operating system and version:

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 AlphaFold2_advanced.ipynb and the prep_filter and trim_inputs entry points in colabfold_alphafold.py, especially the chain parsing around line 409. Reproduce the reported trim_inverse input and inspect how chain identifiers are resolved. Done means the specified antigen epitope trim completes without the reported KeyError and produces results.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook, python
Domain
bioinformatics, machine-learning
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
42/100

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