sokrypton / sokrypton/ColabFold
Index error/ List Index out of range in the Display 3D structure
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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
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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