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. > > <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@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