sokrypton / sokrypton/ColabFold
pdb100_230517_seq does not exist issue
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Description
Hi,
I setup colabfold databases using your setup database script. I ran colabfold-search with —use-templates 1 and provided thet template path with —db2 pdb100_230517_dir/pdb100_230517. I get this error pdb100_230517_dir/pdb100_230517_seq does not exist.
Can you let me know why pdb100_230517_seq is not present in the database directory even though I used your setup database script. I set MMSEQS_NO_INDEX to 1.
Also I am a bit confused with the two pdb databases. I used here pdb100_230517 created from pdb100_230517.fasta.gz for colabfold-search step but where should I use pdb100_foldseek_230517.
Regards
Rakesh
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.
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Research direction
Start with the setup database script and the colabfold-search template-database arguments described in the issue. Check how MMSEQS_NO_INDEX affects generation of pdb100_230517_seq and compare the roles of pdb100_230517 and pdb100_foldseek_230517. Done means explaining or fixing the missing database path and documenting which database each command should use.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, databases
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100