Hi Ed,
The "write" command only allows you to save one model at a time.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>

To save multiple models to one PDB file you have to use the GUI  
("File... Save PDB" or "Actions... Write PDB").
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>

Sorry about that,
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

On Apr 1, 2009, at 1:02 PM, Edward Brignole wrote:

Elaine and co,

I have a mess of models that I'm opening, repositioning a ligand  

using match to various positions in each model. No problem there.  

For each model and ligand position I select the correct chains from  

that model with the repositioned ligand models but can't manage to  

save coordinates. Obviously there's the save pdb dialog but for all  

these models and ligands this will be more convenient scripted into  

chimera commands. I've got it all working except this:

select #6:.a-p #8 #9

write selected relative 0 #6,8,9 /path/to/file.pdb

~select

The part it doesn't like is the model_numbers and I've tried  

various permutations without success. The only way I can get it to  

work is if I only specify one model number.

Can you please help me figure out how to phrase this command  

correctly? An example or two on that commands page might make the  

syntax easier to decipher.

Thank you for your excellent program and support.

Ed

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Edward Brignole

NIH Kirschstein Postdoctoral Fellow

Francisco Asturias Lab, CB227

Center for Integrative Molecular Biosciences

The Scripps Research Institute

www.scripps.edu/~brignole

brignole@scripps.edu

443-653-2070 (cell)

858-784-8598 (lab)

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