Dear Georg,
Have you tried doing Molecular replacement with only the hints that you have got from Mass Spec using AF models? That would give you at least which ones could fit. The most reasonable way to me is to firstly find what is this extra density. Then I would use your 5 chains as a model for MR and then build the extra density with the protein that fits your density when not running your known sample.
Best wishes
______________________________________________________
Rafael Marques da Silva
PhD Student – Structural Biology
University of Leicester
Mestre em Física Biomolecular
Universidade de São Paulo
Bacharel em Ciências Biológicas
Universidade Federal de São Carlos
phone: +44 07861 273773
"A sorte acompanha uma mente bem treinada"
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De: Oleg Sobolev
Dear Phenix community, I have solved the structure of protein complex consisting of 6 chains. We have the structure with 5 chains now and still see positive electron density and mass spec analysis gave us some possible candidates which we would like to model with AF3. However just using MSA's AF3 is not placing two chains correctly, therefore I want to give the structure templates for the 5 chains. However using the proposed way to create the files *https://github.com/google-deepmind/alphafold3/issues/462 * I get an error: ValueError: INVALID_ARGUMENT: The number of values (1958407) in a loop is not a multiple of the number of the loop's columns (19)
However it works if I use 5Y2E.cif from PDB.
Comparing the cif files I see a difference. from phenix: loop_ _atom_site.group_PDB _atom_site.id _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.auth_asym_id _atom_site.auth_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.type_symbol _atom_site.pdbx_formal_charge _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_model_num
from 5Y2E loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num
After processing 5Y2E loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num
Did anybody encountered the same problem and has a workaround?
Additionally I would like to ask if anybody knows which entries of the cif file header are really needed for AF3 to run? I would like to make a google colab which does the processing, without relying on the structure module from AF3 code (from alphafold3 import structure). There is a Python Package with the same name "alphafold3" on PyPi but this does not have a structure subpackage.
Many thanks, br Georg. _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s
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