Displaying multiple sequences during alignment
Hi I have a very quick query. I opened up 3 models - 3cx5, 2qjp and 1zrt in ChimeraX. I was thinking of aligning on one of the chains and looking at the global-sequence-alignment.
match #3/C #2/A to #1/C showAlignment true
The sequence alignment opens up as pairwise sequence alignement, in 2 separate windows for each of the 2 pairs. Picture attached. Rather, is there a way to get all 3 sequences aligned together, not separately? I tried looking up at other options, but I think I am missing out something somewhere. Thanks Yaikhomba
Hi Yaikhomba, Yes, Matchmaker only makes pairwise alignments. Chimera (but not yet ChimeraX) has a Match -> Align tool that, after you have multiple structures superimposed in 3D, then you can calculate the multiple sequence alignment from the spatial information. So currently you would need to use Chimera: first matchmaker to superimpose all three, then Chimera Match->Align (in Chimera menu under: Tools... Structure Comparison) to create the multiple sequence alignment. You could then save the multiple sequence alignment to a file (from the sequence window File menu), then open it in ChimeraX. Chimera Match->Align <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matcha...> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 8, 2021, at 7:19 AM, Y. Mutum <ym337@cam.ac.uk> wrote:
Hi I have a very quick query. I opened up 3 models - 3cx5, 2qjp and 1zrt in ChimeraX. I was thinking of aligning on one of the chains and looking at the global-sequence-alignment.
match #3/C #2/A to #1/C showAlignment true
The sequence alignment opens up as pairwise sequence alignement, in 2 separate windows for each of the 2 pairs. Picture attached.
Rather, is there a way to get all 3 sequences aligned together, not separately? I tried looking up at other options, but I think I am missing out something somewhere. Thanks Yaikhomba
Thank you. Get Outlook for Android<https://aka.ms/ghei36> ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, March 8, 2021 3:31:34 PM To: Y. Mutum <ym337@cam.ac.uk> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Displaying multiple sequences during alignment Hi Yaikhomba, Yes, Matchmaker only makes pairwise alignments. Chimera (but not yet ChimeraX) has a Match -> Align tool that, after you have multiple structures superimposed in 3D, then you can calculate the multiple sequence alignment from the spatial information. So currently you would need to use Chimera: first matchmaker to superimpose all three, then Chimera Match->Align (in Chimera menu under: Tools... Structure Comparison) to create the multiple sequence alignment. You could then save the multiple sequence alignment to a file (from the sequence window File menu), then open it in ChimeraX. Chimera Match->Align <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matcha...> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 8, 2021, at 7:19 AM, Y. Mutum <ym337@cam.ac.uk> wrote:
Hi I have a very quick query. I opened up 3 models - 3cx5, 2qjp and 1zrt in ChimeraX. I was thinking of aligning on one of the chains and looking at the global-sequence-alignment.
match #3/C #2/A to #1/C showAlignment true
The sequence alignment opens up as pairwise sequence alignement, in 2 separate windows for each of the 2 pairs. Picture attached.
Rather, is there a way to get all 3 sequences aligned together, not separately? I tried looking up at other options, but I think I am missing out something somewhere. Thanks Yaikhomba
participants (2)
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Elaine Meng -
Y. Mutum