Hi Harry
Thank you for the information on how hard it is to work locally. I wish
you all the best!
Marta
El 2024-02-23 12:48, Harry Powell escribió:
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://urldefense.com/v3/__https://mmcif.pdbj.org/converter/__;!!D9dNQwwGXtA!XMcmybqK0HPR5lesHR0z2fmHCeayJ5FcnnIgg3d4jkoyOg2CkpZuOjcUUeOrMfxOKrT1yK5tcht0OqR8DJeJA06PTJioAK6PzQ$
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
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Marta Mª Martínez Júlvez
Profesora Titular de Universidad
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Ciencias
Instituto de Biocomputación y Física Sistemas Complejos (BIFI)
Universidad de Zaragoza
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Flavoenzymes: action mechanisms and biotechnology
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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/
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