Hi Ben, Elaine's solution would be done by making a Chimera command file (suffix ".cmd") with lines open 100 allatoms.pdb ; matrixcipy #0 #100 ; close #0 open 101 allatoms.pdb ; matrixcipy #1 #101 ; close #1 open 102 allatoms.pdb ; matrixcipy #2 #102 ; close #2 .... To save some typing you can make a Python script (file suffix ".py") instead like: from chimera import runCommand for i in range(50): runCommand('open %d allatoms.pdb ; matrixcipy #%d #%d ; close #%d' % (100+i, i, 100+i, i)) Opening that file with Chimera File/Open... to replace all your models. Tom Elaine Meng wrote:
On Oct 3, 2008, at 1:31 AM, Benoit Zuber wrote:
I was wondering, if after fitting say 50 Calpha chains I wanted to replace them by the full molecular model (for showing in a talk for example), would there be an easy way to do that?
Hi Ben, This probably does not qualify as easy, but I would just open the full copies and transform them to match their respective alpha-carbon traces, then close the alpha-carbon trace models. Definitely save a session file before doing this part! Something like:
matrixcopy #0 #50 (apply transformation matrix of CA model 0 to full model 50, which assumes their untransformed CA coords are identical) <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html>
or
match #50@ca #0@ca (fit CA atoms of model 50 to those of model 0, which assumes the models have the same number of CA atoms in the same order) <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
then possibly
close 0
You could make a Chimera command file to do all 50. Alternatively, for the programming expert, there must be a sneaky way to substitute the full coordinates of each structure for the CA-trace coordinates within the python session file, but this is beyond my skill set, and session-editing can be a risky sport. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
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