Hi folks I am in the situation of having coordinates of apoproteins (i.e. polypeptide chains without prosthetic groups) in PDB format - but I need them in mmCIF format so I can run them through a locally built copy of AlphaFill.
I need something I can install locally, so web services are a no-no. I’ve tried obabel and Coot to convert the PDB to mmCIF, but AlphaFill doesn’t like the files produced. Before I spend time searching through available options on the interweb, does anyone know of a utility that can provide me with suitable mmCIFs? Note that I *only* have the coordinates because they come from modelling. I’m assuming that I’ve run obabel and Coot correctly! obabel: > alphafill process protein_obabel.cif filled.cif > Structure file does not seem to contain polymers, perhaps > pdbx_poly_seq_scheme is missing? Coot: > alphafill process protein_A-coot-0.cif filled.cif > Error reading file ‘protein_A-coot-0.cif' > >> parse error at line 2: This file does not seem to be an mmCIF file Harry ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
