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 <j.roman.wal...@gmail.com> 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 > <herman.schreu...@sanofi.com> 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 <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Nicholas Keep > Gesendet: Freitag, 27. August 2021 16:51 > An: CCP4BB@JISCMAIL.AC.UK > 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; scid...@bbk.ac.uk > Dept email n.k...@mail.cryst.bbk.ac.uk > 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/
