Re: [ccp4bb] PDB to AlphaFold via Uniprot
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 < 5741fb55e4af-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 > 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 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=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=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=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] PDB to AlphaFold via Uniprot
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 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 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=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=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=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/
Re: [ccp4bb] PDB to AlphaFold via Uniprot
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 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=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=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/
[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=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/
