Hi Paul, You have probably solved this already, but in case you are interested I have written a script to superpose AlphaFold models using PDBe mmCIF annotations, AlphaFold DB and Gemmi (link below), as I had already done something similar in a previous project. It is probably better to use 3D-Beacons as Robbie suggested however as it has a documented API.
https://gist.github.com/paulsbond/e4806e878c578218d0ae56bb5067a330 Cheers, Paul B On Sat, 30 Jul 2022 at 13:45, Nicholas Larsen < 00005741fb55e4af-dmarc-requ...@jiscmail.ac.uk> wrote: > Or you can go straight to uniprot. Every available PDB + alphafold model > is linked to the uniprot entry. > > On Fri, Jul 29, 2022 at 4:46 PM Robbie Joosten <robbie_joos...@hotmail.com> > wrote: > >> Hi Paul, >> >> From the PDB file get the Uniprot primary accession code (see DBREF) and >> use this to get the Alphafold model using 3D-beacons ( >> https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/). >> You can also use 3D-beacons to get the related AlphaFill model (just >> saying...). >> >> Cheers, >> Robbie >> >> > -----Original Message----- >> > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Paul >> > Emsley >> > Sent: Friday, July 29, 2022 20:31 >> > To: CCP4BB@JISCMAIL.AC.UK >> > Subject: [ccp4bb] PDB to AlphaFold via Uniprot >> > >> > I wonder if others are curious about (or know how to solve) the >> > following problem: >> > >> > I am looking at a PDB file that I've downloaded from a wwPDB site and I >> > would like to see the AlphaFold model(s) overlaid. What the best (or >> > easiest) way of doing that? (let's imagine that I can do a bit of >> > scripting in python (including urllib) and can use the functions in Coot >> > for the superposition). >> > >> > Thanks, >> > >> > Paul. >> > >> > ################################################################### >> > ##### >> > >> > 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 >> >> 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/ >> > > > -- > Nick Larsen > Director - Lead Discovery > H3 Biomedicine | an Eisai Oncology Company > 300 Technology Sq #5 > Cambridge, MA 02139 > https://www.h3biomedicine.com/ > > > [This e-mail message may contain privileged, confidential and/or > proprietary information of H3 Biomedicine. If you believe that it has been > sent to you in error, please contact the sender immediately and delete the > message including any attachments, without copying, using, or distributing > any of the information contained therein. This e-mail message should not be > interpreted to include a digital or electronic signature that can be used > to authenticate an agreement, contract or other legal document, nor to > reflect an intention to be bound to any legally-binding agreement or > contract.] > > ------------------------------ > > 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/
