Hi Marta Thanks for this.
Unfortunately, I can’t use a web resource for this - I have to do it locally (partly because I’m providing a web service, and it’s better not to blame other providers when my service fails). I’d be likely to be doing this > 1000 times a day (every day from now until I retire ;-)); I’ve found with other web resources that this can trigger DDOS protection systems (e.g. being temporarily banned…). best wishes Harry > On 23 Feb 2024, at 11:41, Marta Martínez <mmart...@unizar.es> wrote: > > Hi Harry > > I use this link: https://mmcif.pdbj.org/converter/ > > to convert pdb to mmCIF . Hope, it was usuful for your modelled coodinates. > > Regards > > Marta > > > > El 2024-02-23 12:32, Harry Powell escribió: > >> 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://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!D9dNQwwGXtA!QcsCirvGSSOQ779AGoT1ZEsruNSr3LkKxEUfDVhcXI4f1fH72cufVoQcb813Hvn6U2q_rxYvXX8hhDvEioMUjQYnTw5a0hXSwg$ >> >> >> This message was issued to members of >> https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!D9dNQwwGXtA!QcsCirvGSSOQ779AGoT1ZEsruNSr3LkKxEUfDVhcXI4f1fH72cufVoQcb813Hvn6U2q_rxYvXX8hhDvEioMUjQYnTw6gUmC_6A$ >> , a mailing list hosted by >> https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!D9dNQwwGXtA!QcsCirvGSSOQ779AGoT1ZEsruNSr3LkKxEUfDVhcXI4f1fH72cufVoQcb813Hvn6U2q_rxYvXX8hhDvEioMUjQYnTw5AP8cazg$ >> , terms & conditions are available at >> https://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!D9dNQwwGXtA!QcsCirvGSSOQ779AGoT1ZEsruNSr3LkKxEUfDVhcXI4f1fH72cufVoQcb813Hvn6U2q_rxYvXX8hhDvEioMUjQYnTw5DFGTKgA$ > > > -- > Marta Mª Martínez Júlvez > Profesora Titular de Universidad > Departamento de Bioquímica y Biología Molecular y Celular, Facultad de > Ciencias > Instituto de Biocomputación y Física Sistemas Complejos (BIFI) > Universidad de Zaragoza > Pedro Cerbuna 12, 50009-Zaragoza Spain > Phone: 34 976 762841 Fax: 34 976 762123 > e-mail:mmart...@unizar.es > Flavoenzymes: action mechanisms and biotechnology > https://bioquimica.unizar.es/biologia-estructural > http://www.bifi.es/es/biofisica/ ######################################################################## 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/
