[chimera-dev] writing pdb files

[Elaine Meng]

Dear Jim,
If you have a UNIX system, the "pdbrun" command may be able to 
do what you want.  Only the transformed coordinates are written
out.  I recommend the "nouser" keyword to avoid getting a lot of
extra information in USER records.  If there are multiple
models, they all get sent to one file with END records in between
(some postprocessing may be required).
example usage: pdbrun all nouser cat >file.pdb     See

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/pdbrun.html

The "write" command is much better for this purpose (and works for
all of the platforms) but is not in the current release.
It has been implemented in our working version and will be available
in the next release.  See

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html

I am not sure when the next release will come out, however.

Finally, I believe there is a way to get the transformation matrices
but I must defer to the programmers on the team to address this point.
I hope this helps,
Elaine
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Elaine C. Meng, R.Ph., Ph.D.
Babbitt Lab and Computer Graphics Lab
meng at cgl.ucsf.edu
http://www.cgl.ucsf.edu/home/meng/index.html
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