Hi Zaher, Forgot to answer the other part of your question. In ChimeraX, currently the Matchmaker tool is in the menu under Tools... Structure Analysis, and there is also a "matchmaker" or "mmaker" command. Command syntax is slightly different than in Chimera, as we tried to improve many commands. <http://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> There is another mailing list chimerax-user@cgl.ucsf.edu specifically for ChimeraX, if you are interested! I hope this helps, Elaine
On Sep 18, 2020, at 11:53 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Yes, the Matchmaker dialog does have a choice to show the pairwise alignments, but the option that I mentioned is a different one. As I said, it starts the Match->Align tool. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html#final>
ChimeraX does not yet have anything like the Match->Align tool, sorry.
Elaine
On Sep 18, 2020, at 11:39 AM, arrafzaher@campus.technion.ac.il wrote:
Thank you Elaine, I know about the choice in the MM dialog however this runs 2 separate MSA.
The first method helped, where can I find these tools in ChimeraX?
Zaher On 18/09/2020, 19:44, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
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.
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
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