Updating pdb SEQRES record with a loaded .fasta file
Hello, I would like to use a .fasta file that I have loaded into ChimeraX to update the SEQRES records of a PDB file that is also loaded into ChimeraX. Currently the loaded PDB file only has SEQRES records for the residues that are modelled, while the .fasta file has the full, sequence with no gaps. I have tried loading in the .fasta file and then using the $ sequence associate command to associate it with the relevant pdb chain. However, when I then save out the pdb file (using the $ save command) and then examine the pdb file it still only records the modelled residues. Is there any way to force the written pdb file to have the full sequence as uploaded in the .fasta file? I am running chimeraX version 1.7 (2023-12-19). Thanks for your help, Sam Samuel Haysom Research Scientist • Biophysics Nxera Pharma UK Limited +44 (0)1223 949201 • Steinmetz Building, Granta Park, Great Abington Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Nxera Pharma UK Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.
Hi Sam, Associating a chain to an alignment sequence doesn’t change ChimeraX’s opinion of what the chain's sequence is, since there are various reasons you might what to associate a chain to what might be only a similar sequence. Nonetheless, what you want to do is pretty useful, so I will try to add support for it in the sequence viewer sometime soonish. In the interim you can get what you want by running the attached script, which will transfer alignment sequences to each associated chain. You run the script simply by opening it (“open /where/you/saved/xfer-seq.py”). --Eric Eric Pettersen UCSF Computer Graphics Lab 
On Jun 10, 2024, at 3:05 AM, Samuel Haysom via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I would like to use a .fasta file that I have loaded into ChimeraX to update the SEQRES records of a PDB file that is also loaded into ChimeraX. Currently the loaded PDB file only has SEQRES records for the residues that are modelled, while the .fasta file has the full, sequence with no gaps. I have tried loading in the .fasta file and then using the $ sequence associate command to associate it with the relevant pdb chain. However, when I then save out the pdb file (using the $ save command) and then examine the pdb file it still only records the modelled residues. Is there any way to force the written pdb file to have the full sequence as uploaded in the .fasta file?
I am running chimeraX version 1.7 (2023-12-19).
Thanks for your help, Sam
Samuel Haysom <mailto:Samuel.Haysom@nxera.life> Research Scientist • Biophysics Nxera Pharma UK <https://nxera.life/> Limited
+44 (0)1223 949201 • Steinmetz Building, Granta Park, Great Abington Cambridge, CB21 6DG, United Kingdom

The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Nxera Pharma UK Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Eric, Yep that makes sense, as you said it would be nice to have a separate command to do it. Thanks for the script this will be very helpful! KR, Sam Samuel Haysom Research Scientist • Biophysics Nxera Pharma UK Limited +44 (0)1223 949201 • Steinmetz Building, Granta Park, Great Abington Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Nxera Pharma UK Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989. ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Monday, June 10, 2024 21:18 To: Samuel Haysom <Samuel.Haysom@Nxera.life> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Updating pdb SEQRES record with a loaded .fasta file Hi Sam, Associating a chain to an alignment sequence doesn’t change ChimeraX’s opinion of what the chain's sequence is, since there are various reasons you might what to associate a chain to what might be only a similar sequence. Nonetheless, what you want to do is pretty useful, so I will try to add support for it in the sequence viewer sometime soonish. In the interim you can get what you want by running the attached script, which will transfer alignment sequences to each associated chain. You run the script simply by opening it (“open /where/you/saved/xfer-seq.py”). --Eric Eric Pettersen UCSF Computer Graphics Lab On Jun 10, 2024, at 3:05 AM, Samuel Haysom via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hello, I would like to use a .fasta file that I have loaded into ChimeraX to update the SEQRES records of a PDB file that is also loaded into ChimeraX. Currently the loaded PDB file only has SEQRES records for the residues that are modelled, while the .fasta file has the full, sequence with no gaps. I have tried loading in the .fasta file and then using the $ sequence associate command to associate it with the relevant pdb chain. However, when I then save out the pdb file (using the $ save command) and then examine the pdb file it still only records the modelled residues. Is there any way to force the written pdb file to have the full sequence as uploaded in the .fasta file? I am running chimeraX version 1.7 (2023-12-19). Thanks for your help, Sam Samuel Haysom<mailto:Samuel.Haysom@nxera.life> Research Scientist • Biophysics Nxera Pharma UK<https://eu-west-1.protection.sophos.com?d=nxera.life&u=aHR0cHM6Ly9ueGVyYS5sa...> Limited +44 (0)1223 949201 • Steinmetz Building, Granta Park, Great Abington Cambridge, CB21 6DG, United Kingdom [cid:bdc07a81-c548-461e-80c9-94de8a0611de@GBRP265.PROD.OUTLOOK.COM] The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Nxera Pharma UK Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/<https://eu-west-1.protection.sophos.com?d=ucsf.edu&u=aHR0cHM6Ly9tYWlsLmNnbC51Y3NmLmVkdS9tYWlsbWFuL2FyY2hpdmVzL2xpc3QvY2hpbWVyYXgtdXNlcnNAY2dsLnVjc2YuZWR1Lw==&i=NjM3OThiYWVjY2IxZGExM2JmY2IyN2I3&t=UHpDZ25pd3F0U3UzY1J4dmpPYkdnSkVQaFg3SE9ldXl0SDJueVhzc3RkTT0=&h=81a4e30b7b0248c69131542552a79d7c&s=AVNPUEhUT0NFTkNSWVBUSVZ01BlPSxPlgFK41ClAmcEJeb9m046-d9bjC4OfevchkQ>
Hi Sam, Today's daily build has a command (sequence update) for setting the chain sequence from an alignment sequence. Help page: Command: sequence <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sequence.html#update>. There is also a Structure→Update Chain Sequence... menu item in the sequence viewer context menu for doing the same thing.. --Eric
On Jun 12, 2024, at 6:45 AM, Samuel Haysom via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Eric,
Yep that makes sense, as you said it would be nice to have a separate command to do it. Thanks for the script this will be very helpful!
KR, Sam
Samuel Haysom <mailto:Samuel.Haysom@nxera.life> Research Scientist • Biophysics Nxera Pharma UK <https://nxera.life/> Limited
+44 (0)1223 949201 • Steinmetz Building, Granta Park, Great Abington Cambridge, CB21 6DG, United Kingdom
<image990637.png>
The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Nxera Pharma UK Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989. From: Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Sent: Monday, June 10, 2024 21:18 To: Samuel Haysom <Samuel.Haysom@Nxera.life <mailto:Samuel.Haysom@Nxera.life>> Cc: chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] Updating pdb SEQRES record with a loaded .fasta file
sophospsmartbannerend Hi Sam, Associating a chain to an alignment sequence doesn’t change ChimeraX’s opinion of what the chain's sequence is, since there are various reasons you might what to associate a chain to what might be only a similar sequence. Nonetheless, what you want to do is pretty useful, so I will try to add support for it in the sequence viewer sometime soonish. In the interim you can get what you want by running the attached script, which will transfer alignment sequences to each associated chain. You run the script simply by opening it (“open /where/you/saved/xfer-seq.py”).
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 10, 2024, at 3:05 AM, Samuel Haysom via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello,
I would like to use a .fasta file that I have loaded into ChimeraX to update the SEQRES records of a PDB file that is also loaded into ChimeraX. Currently the loaded PDB file only has SEQRES records for the residues that are modelled, while the .fasta file has the full, sequence with no gaps. I have tried loading in the .fasta file and then using the $ sequence associate command to associate it with the relevant pdb chain. However, when I then save out the pdb file (using the $ save command) and then examine the pdb file it still only records the modelled residues. Is there any way to force the written pdb file to have the full sequence as uploaded in the .fasta file?
I am running chimeraX version 1.7 (2023-12-19).
Thanks for your help, Sam
Samuel Haysom <mailto:Samuel.Haysom@nxera.life> Research Scientist • Biophysics Nxera Pharma UK <https://eu-west-1.protection.sophos.com/?d=nxera.life&u=aHR0cHM6Ly9ueGVyYS5s...> Limited
+44 (0)1223 949201 • Steinmetz Building, Granta Park, Great Abington Cambridge, CB21 6DG, United Kingdom
<image779816.png>
The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Nxera Pharma UK Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ <https://eu-west-1.protection.sophos.com/?d=ucsf.edu&u=aHR0cHM6Ly9tYWlsLmNnbC...> _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/>
participants (2)
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Eric Pettersen -
Samuel Haysom