[Chimera-users] matchmaker and MSA

[Elaine Meng]

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 at 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 at 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 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
>>> 
>> 
>>   This email is from an external mail server, be judicious when opening attachments or links
>> 
>> 
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> 
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