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! <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#command> 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. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/history.html> Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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