[Chimera-users] matchmaker and MSA

[arrafzaher at campus.technion.ac.il]

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