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


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:

--Jeff Van Voorst

Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

My other email account has a "professional" signature.