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<mailto:scid...@bbk.ac.uk> Dept email n.k...@mail.cryst.bbk.ac.uk<mailto: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<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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/<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/
