sokrypton / sokrypton/ColabFold

How to use templates found by mmseqs

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Description

If you run colabfold_search with --use-templastes 1 option, it will generate a single .m8 file containing the template hits as well as MSAs. I am wondering how I can make colabfold_batch to use this file?

In details, Running this:

 colabfold_search --threads 
  --db2 pdb70_220313 \
  --use-templates 1 \
  --use-env 1 \
  --db-load-mode 0 \
  fasta \
  $DATA_DIR \
  msas

would result in the following files in the msas directory:

0.a3m
1.a3m
2.a3m
3.a3m
4.a3m
5.a3m
6.a3m
7.a3m
8.a3m
9.a3m
...
pdb70_220313.m8

There is also pdb directory containing containing .cif.gz files, downloaded with setup_databases.sh script, which can be used.

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by tracing the colabfold_search output, the pdb70_220313.m8 file, and how colabfold_batch consumes files in the msas and pdb directories. Review the setup_databases.sh workflow and document the supported steps for using the generated template hits, including an example command and what output indicates success.

Written by the indexing model from the issue text.

Assessment

Domain
bioinformatics, cli
Issue type
Documentation
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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