Hi Jon Just checked an mmCIF file for one of the AlphaFold models - the model number is “1”, no sign of a model 0 that I can see…
A quick “sed” script could sort them all out… Harry > On 10 Nov 2021, at 12:22, Jon Agirre <[email protected]> wrote: > > It might be, because the mmCIF versions work fine with MG. > > On Wed, 10 Nov 2021 at 12:16, Harry Powell - CCP4BB > <[email protected]> wrote: > Hi folks > > Been a while, but I’ve been doing some work on checking that some files are > valid PDB files and went back to the documentation; as far as I can work out, > the best solution to this is John Walker’s, because “MODEL 0” is not allowed > in the standard (maybe it is for mmCIF…) - > > > On 27 Aug 2021, at 16:39, John R. Walker <[email protected]> wrote: > > > > I just change MODEL 0 to MODEL 1 then it works fine. > > > > John > > As far as I can see (from a small sample of the 150,000 AlphaFold models, > soon to be a few more...) all the PDB files downloadable from > alphafold.ebi.ac.uk are non-conformant. The documentation on PDB files that I > have been able to find easily says - > > > Details > > > > * This record is used only when more than one model appears in an entry. > > Generally, it is > > employed only for NMR structures. The chemical connectivity should be the > > same for each model. > > ATOM, HETATM, SIGATM, SIGUIJ, ANISOU, and TER records for each model > > structure are > > interspersed as needed between MODEL and ENDMDL records. > > > > * The numbering of models is sequential beginning with 1. > > Harry > > > > > On Fri, Aug 27, 2021 at 11:03 AM Schreuder, Herman /DE > > <[email protected]> wrote: > > Dear Nick, > > > > > > > > I had just looked at a pdb downloaded from the alphafold server without > > problems. However, then I realized that I had looked at the alphafold model > > after I had it superimposed on my own structure. Loading the alphafoldmodel > > directly in coot failed for me as well. > > > > > > > > By looking into the pdb file, I discovered that the alphafold file has a > > “MODEL” record just before the coordinates and an “ENDMDL” record after the > > coordinates. After deleting these two records, the alphafold pdb loads fine. > > > > > > > > Hope this helps, > > > > Herman > > > > > > > > Von: CCP4 bulletin board <[email protected]> Im Auftrag von Nicholas > > Keep > > Gesendet: Freitag, 27. August 2021 16:51 > > An: [email protected] > > Betreff: Re: [ccp4bb] A "funny" thing related to AlphaFold2 .... > > > > > > > > Has anyone made use of an Alpha Fold PDB as opposed to CIF. On the half > > dozen or so I have tried to read into CCP4mg or coot the PDB has always > > failed but the CIF is fine. I can then write out a PDB if I want. > > > > I could add to the conspiracy theories that this is EBI trying to > > normalise use of CIF format, but I suspect it is something much more > > mundane, that should be addressed. > > > > Best wishes > > > > Nick > > > > -- > > NOTE NEW PHONE NUMBER JULY 2020 > > > > I do not work Mondays. For urgent business on a Monday contact Clare > > Woodward (Director of Operations) or Gillian Forrester (Deputy Dean) > > > > Prof Nicholas H. Keep > > Executive Dean of School of Science > > Professor of Biomolecular Science > > Crystallography, Institute for Structural and Molecular Biology, > > Department of Biological Sciences > > Birkbeck, University of London, > > Malet Street, > > Bloomsbury > > LONDON > > WC1E 7HX > > > > Office G54a > > > > Dean Email; [email protected] > > Dept email [email protected] > > Telephone 020-3926-3475 (Will contact me at home if working as well as my > > office) > > > > If you want to access me in person you have to come to the crystallography > > entrance > > and ring me or the department office from the internal phone by the door > > > > ######################################################################## > > > > 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 > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > ######################################################################## > > 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/ > > > -- > Dr Jon Agirre > Royal Society Olga Kennard Research Fellow > York Structural Biology Laboratory / Department of Chemistry > University of York, Heslington, YO10 5DD, York, UK > http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ > Office: /B/K/065 Phone: +44 (0) 1904 32 8252 > Twitter: @glycojones > ######################################################################## 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/
