[Chimera-users] Matchmaker & fit map into map

Hernando J Sosa hernando.sosa at einstein.yu.edu
Wed Aug 16 15:19:50 PDT 2017


Hi Elaine


>(2) use “matrixcopy” command to apply rotation/translation matrix from structure #2 to map #3:
>matrixcopy #2 #3

did the trick for me. Thanks! (much better than trying to fit manually map into map each time). I will try ChimeraX later.

Best

H.

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Wednesday, August 16, 2017 1:54 PM
To: Hernando J Sosa
Cc: chimera-users at cgl.ucsf.edu BB
Subject: Re: [Chimera-users] Matchmaker & fit map into map

Hi Hernando,
In our newer software ChimeraX, there is a matchmaker command “bring” option that does exactly what you describe:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>

However, Chimera does not have this matchmaker option, and things may be more complicated.

If the map and its atomic structure are already in the right relationship with each other when you first open their files, it should work to:

(1) superimpose the atomic structure (let’s call it model #2) onto another atomic structure (#1) 

(2) use “matrixcopy” command to apply rotation/translation matrix from structure #2 to map #3:
matrixcopy #2 #3
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html>

However, if the map and its structure weren’t in the right relationship when their files were first opened (if you had to move them separately, e.g. fitting), I don’t think that would work.  

The Chimera “match” (but not matchmaker) command does have an “active” option to bring other models that are activated for motion (movable with the mouse) along during the match.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 16, 2017, at 6:15 AM, Hernando J Sosa <hernando.sosa at einstein.yu.edu> wrote:
> 
> Dear Chimera,
> 
> Is it possible when using Matchmaker to move an associated density map with it?
> Eg:  assuming that atomic model #1 is fitted to density  #2 and  atomic model #3 is fitted to density #4,  is it possible to move/match #3 into #1 moving #4 with it? 
> I know it would be possible to achieve something similar doing Matchmaker first and then fit map into map, but I wonder if  the above could be done too as it would be simpler and easier when dealing with many maps with already fitted structures.
> 
> Thanks
> Hernando




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