[Chimera-users] matchmaker and MSA
meng at cgl.ucsf.edu
Fri Sep 18 11:53:45 PDT 2020
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.
ChimeraX does not yet have anything like the Match->Align tool, sorry.
> On Sep 18, 2020, at 11:39 AM, arrafzaher at 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?
> On 18/09/2020, 19:44, "Elaine Meng" <meng at 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.
>> On Sep 18, 2020, at 9:39 AM, Elaine Meng <meng at 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 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 at campus.technion.ac.il wrote:
>>> 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.
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