[Chimera-users] Matchmaker & fit map into map

Tom Goddard goddard at sonic.net
Wed Aug 16 11:56:30 PDT 2017

Hi Hernando,

  The trick you want is to use “matrixcopy” with the “moving” option to move additional models using the same motion.  First matchmaker an extra copy of the atomic model (#5) then move the original copy (#3) and associated density map (#4) to align with it

	matchmaker #1 #5
  	matrixcopy #5 #3 moving #4

https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html>


> On Aug 16, 2017, at 10:54 AM, Elaine Meng  wrote:
> 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  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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