[chimera-dev] Accessing rotation matrix of molecule models

Elaine Meng meng at cgl.ucsf.EDU
Thu Jul 18 16:34:24 PDT 2002

Hello Mike,
We haven't yet implemented the matrixget/matrixset commands that were
in the predecessor program Midas.  The write command just got implemented
but is not in the released version (it will be in the next release).

In the meanwhile, I can think of a few possibilities:

  (1) individual distances can be measured manually within Chimera
   ("distance" command or Controllers...Distances)

  (2) if you are on unix, the "pdbrun" command can be used to send out
   the coordinates of everything that is displayed.  Note that the
   coordinates of both structures would be transformed, but you would
   be able to use these coordinate sets for the position of one relative
   to the other.  The command would look something like
        pdbrun nouser cat > bothstructures.pdb
   You would have to make sure that all the atoms you want the coordinates
   of in the file bothstructures.pdb are displayed. 
   All displayed models are in the output file, with END between them;
   you might need to make separate files out of this output file, depending
   on what you want to do next.

  (3) there is probably some not too complicated way to get and apply
   the transformation matrices out using the Python interface or a Python
   script, but I am not skilled in this area - other members of the development
   team could probably give you more details. 

I hope this helps.  Anybody else with current solutions, please chime in...
In the next version, I think the simplest way would be to use the "write"
command to save the coordinates of one model relative to those of the other.  
Elaine C. Meng, R.Ph., Ph.D.
Babbitt Lab and Computer Graphics Lab
meng at cgl.ucsf.edu

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