sokrypton / sokrypton/ColabFold

Index error/ List Index out of range in the Display 3D structure

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Jupyter Notebook
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Description

Expected Behavior

I am trying to use my own template (single PDB in a mmcif format) with single_sequence (msa_mode).

I get the following error in the Display 3D Structure cell:

IndexError Traceback (most recent call last)
in ()
46
47
---> 48 show_pdb(rank_num,show_sidechains, show_mainchains, color).show()
49
50

in show_pdb(rank_num, show_sidechains, show_mainchains, color)
19 model_name = f"rank_{rank_num}"
20 view = py3Dmol.view(js='https://3dmol.org/build/3Dmol.js',)
---> 21 view.addModel(open(pdb_file[0],'r').read(),'pdb')
22
23 if color == "lDDT":

IndexError: list index out of range

Steps to Reproduce (for bugs)

Seq: PHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYWERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEGRDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGN:FAPGVFPYM

job_name: test
template mode: custom
Upload the template: 1bz9.cif (downloaded in PDB)

msa_mode: single_sequence
pair Mode: Unpaired+Paired

model_type : auto

Context

Trying to set this PDB as initial guess.

Can you please help resolve this?
Thanks!

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 Display 3D Structure cell and the show_pdb function shown in the traceback. Reproduce the job using the 1bz9.cif custom template and inspect why pdb_file has no first element before view.addModel is called. Done means the structure displays without an IndexError for this setup.

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
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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