sokrypton
Implement initial guess feature
Hi,
This pull request implements the --initial-guess feature, inspired by the functionality available in ColabDesign.
Related issue:
- #432
Description:
-
It enables the handling of protein structure inputs (
.pdband.cif) - using alphafold parser -
The introduction of the
--initial-guessflag allows for the utilization of protein structure atom positions as input. This can be achieved either through the primary input or by specifying the structure input after the--initial-guessflag. -
Minor adjustments to the Alphafold code have been made to accommodate this new feature:
-
https://github.com/steineggerlab/alphafold/pull/8
This update enables the handling of protein structure inputs (.pdb and .cif) using the AlphaFold parser.
- You can now use ColabFold with .pdb or .cif input
- You can use the
--initial-guessflag in the following ways:- Provide a sequence from a .pdb or .cif file and add the flag to use coordinates for the initial guess:
colabfold_batch test.pdb out/ --initial-guess - Add a .fasta file as input, utilizing the RFdiffusion polyglycine backbone as the initial guess:
colabfold_batch test.fasta out/ --initial-guess backbone.pdb
- Provide a sequence from a .pdb or .cif file and add the flag to use coordinates for the initial guess:
Without and with initial guess
@sokrypton Initial guess would be super cool to have also in base colabfold, not just colabdesign.
@ajasja Have you tried AlphaPulldown? Looks like it has a feature (TrueMultimer) where you can give a custom template (cif/pdb file).
@Poko18 could you please check if it works as intended? I had to move things around.
Initial guess is working, although we are unable to use pdb/cif files as an input anymore (instead of .fasta, .csv ...). Not sure if this was intended or not
@Poko18 Thank you for checking it! I tried it the following colabfold_batch 7FI4.pdb tmp and it worked.
What command did you use?