Hi.

I'm sorry I didn't respond earlier. I wasn't well. 

Thank you for all of your replays. Jeff Van Voorst's solution was the one I was looking for. 

Again. Thank and sorry

Yotam

On Mon, Jun 18, 2012 at 6:00 PM, Jeffrey Van Voorst <vanv0059@umn.edu> wrote:
Hello Yotam,

You can place the commands you would otherwise type in the pymol command
window in a .pml file.  Supposing you have a script called
my_script.pml, you can run the script by typing "pymol my_script.pml"
when you start pymol or if you have pymol already running you may use
"@my_script.pml" (without the quotes).

One place this information may be found is:
http://pymol.sourceforge.net/newman/user/S0210start_cmds.html

--Jeff Van Voorst

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