[Chimera-users] how to run the command line chimera without actually opening the GUI

Eric Pettersen pett at cgl.ucsf.edu
Thu Oct 20 15:39:07 PDT 2011

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 Pettersen
                         UCSF Computer Graphics Lab

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