Dear Harry, You can try to read your PDB file and save it as mmCIF using gemmi: https://gemmi.readthedocs.io/en/latest/mol.html#reading
https://gemmi.readthedocs.io/en/latest/mol.html#id3 Best wishes, Martin On Fri, 2024-02-23 at 11:32 +0000, Harry Powell wrote: > 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/ ######################################################################## 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/
