[Chimera-users] matchmaker and MSA

[Elaine Meng]

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 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?
> 
> Zaher
> 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.
>    Elaine
> 
>> 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.
>> 
>> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fmatchalign%2Fmatchalign.html&data=02%7C01%7Carrafzaher%40campus.technion.ac.il%7C6bfd0bf57da34de4df1a08d85bf20ba5%7Cf1502c4cee2e411c9715c855f6753b84%7C1%7C0%7C637360442425122795&sdata=elzHUJySn9pfNK%2FBEBjGs5aI5OX4XLEf77c9aJNZpPM%3D&reserved=0>
>> 
>> 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 at 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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