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