Aligning fasta sequence with the sequence of pdb model in chimeraX
Hi, I was wondering if there is a way in chimeraX to align fasta sequence with sequence from the loaded pdb model. Just wanted to be sure that the residue numbering matches the original Uniprot sequence. Any other suggestions that can do the job quickly are welcome. Best, Rayees
Hi Rayees, Yes, you can do it by (1) showing sequence of the open PDB chain (2) using command "sequence align" to specify aligning the already-shown sequence from the structure + Uniprot sequence. You don't need a fasta file, you could fetch it directly from Uniprot. Example commands open 2gbp, show chain A sequence from it, then align to Uniprot P0AEE5. To specify the already-shown sequence, you use the "alignment" ID as shown in the sequence window title bar and the sequence ID in the alignment.: open 2gbp seq chain /A ... sequence window title bar shows alignment ID: 1/A, and the sequence ID is 1 because it's the first/only sequence in that window ... seq align 1/A:1,P0AEE5 For more explanation of command syntax and options, see help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#align> Then you get a new alignment window with the two sequences aligned. See attached screenshot. You can mouse over the structure sequence to get a pop-up of the associated residue number in the structure. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 20, 2025, at 5:53 PM, Rayees Mattoo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I was wondering if there is a way in chimeraX to align fasta sequence with sequence from the loaded pdb model. Just wanted to be sure that the residue numbering matches the original Uniprot sequence. Any other suggestions that can do the job quickly are welcome.
Best, Rayees_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Great! Thanks. Best ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, February 20, 2025 6:12 PM To: Rayees Mattoo <rmattoo@stanford.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Aligning fasta sequence with the sequence of pdb model in chimeraX Hi Rayees, Yes, you can do it by (1) showing sequence of the open PDB chain (2) using command "sequence align" to specify aligning the already-shown sequence from the structure + Uniprot sequence. You don't need a fasta file, you could fetch it directly from Uniprot. Example commands open 2gbp, show chain A sequence from it, then align to Uniprot P0AEE5. To specify the already-shown sequence, you use the "alignment" ID as shown in the sequence window title bar and the sequence ID in the alignment.: open 2gbp seq chain /A ... sequence window title bar shows alignment ID: 1/A, and the sequence ID is 1 because it's the first/only sequence in that window ... seq align 1/A:1,P0AEE5 For more explanation of command syntax and options, see help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#align> Then you get a new alignment window with the two sequences aligned. See attached screenshot. You can mouse over the structure sequence to get a pop-up of the associated residue number in the structure. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco [cid:dfaa850c-4714-4f8c-823a-6c6dc5c50a28@namprd02.prod.outlook.com]
On Feb 20, 2025, at 5:53 PM, Rayees Mattoo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I was wondering if there is a way in chimeraX to align fasta sequence with sequence from the loaded pdb model. Just wanted to be sure that the residue numbering matches the original Uniprot sequence. Any other suggestions that can do the job quickly are welcome.
Best, Rayees_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (2)
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Elaine Meng -
Rayees Mattoo