[Chimera-users] scripts in Chimera

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 29 14:54:48 PDT 2008

Hi Ben,
Just put the same exact commands you type into a file named  
something.com or something.cmd  - later you can simply open the file  
to execute the commands.  In fact, this exact approach is taken in the  
ViewDock tutorial!

You can make the Chimera command file with a text editor, or open  
Command History (arrow to right of command line, choose Command  
History), select a bunch of previously used commands with the mouse,  
and "Record..." to a file.

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 29, 2008, at 2:43 PM, Ben Keshet wrote:

> Hi,
> I am reviewing a large number of structures (docking results).  I uses
> the ViewDock tool which is great and makes life much easier.  Still,  
> for
> every file I open with ViewDock, I repeat the same set of commands
> before actually reviewing the poses, that is (initially only the
> receptor structure is open, with only ribbon shown):
> 1. open the ligands mol2 file.
> 2. color by element
> 3. choose atoms within 6A from the ligands (by selecting the ligand,
> than select zone<6A).
> 4. show the selected atoms.
> This is to show only receptor atoms within 6A of the ligand.  Is  
> there a
> way I can "record" this sequence or write some simple script that I
> could run after opening the ligands mol2 file?
> Thanks!
> Ben

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