[chimera-dev] Accessing rotation matrix of molecule models
meng at cgl.ucsf.EDU
Thu Jul 18 16:34:24 PDT 2002
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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