Comments (17)
Has this feature been implemented yet?
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We use the partial charge and Hydrogen atoms added by pdb2pqr to engineer a data structure to train CNN models. However, we are trying to switch our data engineering infrastructure to mmCIF files instead of pdb files bc they are more generic and pdb is being deprecated. Switching our infrastructure from pdb to mmCIF files is contingent on generating the partial charges and the SASA values for each atom.
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Nathan,
I totally understand! How long do you believe this cloud migration will take?
Danny
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@danny305 - we're more-or-less moved into the cloud now. Can you please provide a minimal example of the functionality you're hoping for with mmCIF?
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We would like to run your software where we feed in either a pub-redo file or a mmCIF/cif file of a protein and receive back a mmCIF/cif file that has appended the hydrogen atom rows, and a pqr and radius column. Essentially what @speleo3 eloquently summarized.
Additionally, we are having problems obtaining the pqr values for atoms that do not begin with ATOM in the current pdb pipeline. So all atoms that are under HETATM do not get their hydrogen atoms, radius, and pqr value filled in. This includes all ligands and sugars. Could this be addressed in the new mmCIF/cif functionality?
Does this answer your minimal example question?
Danny
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Yes, that works. Thanks for the update.
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Will you guys extend the pqr functionality to non-protein atoms (water, ligands, sugars, chemical modifications, etc)? Or should we prioritize obtaining partial charge for non-protein atoms else where?
I am asking because we are currently trying to address this issue and would like to divert our efforts else where pqr (you guys) could solve this. Please let me know so we can reprioritize our short term development goals.
Danny
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Hi @sobolevnrm
I'm working with Danny on the same project, and I'm happy to help with providing some test cases. I've attached a few cif files that were converted from pdb redo files (also included are the source pdb files). The tool used for the conversion is the Gemmi library (found here).
Please let me know if this is what you're looking for. If it is not, I will gladly provide you with what will help.
Thanks,
James
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Has this been approved/resolved?
Danny
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Yes, thank you.
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Oops... @speleo3 just told me I totally misunderstood this issue and the original intent was to have PDB2PQR produce mmCIF that APBS and other programs could consume.
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