Here is the an example of how to do this in Tcl:
set PYMOL [open "|pymol -pq " w]
puts $PYMOL "viewport 400,400"
puts $PYMOL "load file.pdf"
puts $PYMOL "hide all"
puts $PYMOL "show ribbon"
puts $PYMOL "color blue"
puts $PYMOL "zoom"
flush $PYMOL
puts $PYMOL "color red"
flush $PYMOL
puts $PYMOL "hide all"
puts $PYMOL "show spheres"
puts $PYMOL "color lime"
flush $PYMOL
Here is a page describing the command line options:
http://www.pymolwiki.org/index.php/Command_Line_Options
I used -p and -q above. From the above link:
-q Quiet launch. Suppress splash screen & other chatter.
-p Listen for commands on standard input.
One can use the normal PyMOL commands/settings as well. See the
PyMOLWiki for more info, such as this list of settings:
http://www.pymolwiki.org/index.php/Settings
I'm sure there at Python equivalents for Tcl's open, puts and flush.
I could try to figure these out if you would like.
Doug
On Oct 27, 2006, at 11:29 AM, Edward d'Auvergne wrote:
On 10/28/06, Douglas Kojetin <douglas.kojetin@xxxxxxxxx> wrote:
Hi Edward-
I am able to feed commands into PyMOL from Tcl/Tk scripts through the
use of UNIX pipes. From within the Tcl/Tk script, a pipe is opened
to PyMOL, and the script sends commands to PyMOL. I can tell PyMOL
to open a PDB file, display it in a certain way (cartoon, ribbon),
highlight certain atoms or residues (by sticks, spheres, etc.), color
them, etc. I've never tried writing images, but I don't think it
would be too difficult. Is this the type of functionality you are
looking to incorporate into relax?
This is exactly what is needed. I didn't realise it accepted commands
from STDIN, I told you I didn't look very hard! That makes things
very easy to implement. Is there documentation for this interface?
Are they python commands you send?
Edward
Re: Representing the Brownian rotational diffusion tensor in Molmol, etc.