On Oct 20, 2011, at 11:46 AM, Tom Goddard wrote:

  Here are two problems.  1) The Chimera command script always writes 
the same file "aligned.pdb".  There is no way I could see to specify the 
output file name in the command or have it write "aligned_3h47.pdb", or 
any other name that depends on the input files.

That's true, though typically after the "chimera --nogui ..." command you when then just do "mv aligned.pdb bettername.pdb" using whatever scripting magic your shell supports.

2) You asked that both 
the aligned model and reference model are written to one PDB file.  The 
Chimera "write" command can only write one model to a PDB file (although 
a Chimera dialog can write both).

Right.  Might get improved someday.

--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu