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ihmwg / modelcif_utils

Utilities that support ModelCIF
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mmCIF converter for Multi-chain models #1

Open yakomaxa opened 1 year ago

yakomaxa commented 1 year ago

Thank you for useful script. Do you have any plan to extend the alphafold_pdb_to_cif.py script to multi-chain (oligomer) inputs? I've just modified your script for multi-chain input, but I'm not sure what to be done to satisfy model-cif specification. If it's possible that we refine it to satisfy the specification, I would like to make a pull-request to add multi-chain pdb-cif converter. Thank you.

brindakv commented 1 year ago

@yakomaxa Software support for ModelCIF is provided using python-modelcif. This utility was a created from a precursor to python-modelcif.

You can sure create a PR for the multi-chain variant of this utility. I can review it.

To validate an mmCIF file against a dictionary, use the mmCIF Dictionary Suite. Follow the instructions in the README and use the latest ModelCIF dictionary in step 3.

yakomaxa commented 1 year ago

@brindakv

Thank you for your response and links for resources.

I believe that python-modelcif is more general-purpose mode-cif utility, but I found the script in this repo very useful to concatenate AlphaFold outputs (pdb and pkl containing scores) into a cif file for post-prediction analysis. Although there're some other utilities to un-pickle the scores, merging coordinates and score as a model-cif eases analysis and sharing since it becomes portable as a single file.

After I clean up the modified script and check the output against the dictionary, I will make a pull-request. I appreciate that you will review it.