[Chimera-users] Matchmaker & fit map into map

[Tom Goddard]

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>

   Tom


> 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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