There is also a choice on the Matchmaker dialog to open Match->Align, "After superposition, compute structure-based multiple sequence alignment." That just starts the tool, exactly the same as choosing it from the Tools menu. Elaine
On Sep 18, 2020, at 9:39 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Zaher, Yes, but it is a separate step. After all three structures are superimposed in 3D (using Matchmaker or any other method you like), then you can use the Match->Align tool to create a sequence alignment of all three. Menu: Tools... Structure Comparison... Match->Align.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 18, 2020, at 9:19 AM, arrafzaher@campus.technion.ac.il wrote:
Hi, Suppose I have 3 structures #0 #1 and #2. If I impose structure alignment of both #1 and #2 to #0. I receive two MSA alignment. Is there a way to view one MSA of the 3 structures and not 2 MSA of them. Thanks, Zaher