On Mon, Sep 12, 2011 at 10:05 AM, Thomas Holder <firstname.lastname@example.org>
PyMOL understands two languages. The "PyMOL language" is indeed similar to gnuplot commands, that's what you usually type into the PyMOL command prompt or put into .pml script files.
I'm sorry but this is too complected. Currently, I can't afford the time to learn another scripting languish. Consider gnuplot script files, which are simply a list of gnuplot commands.
The other language is pure python (PyMOL API) and can be used to write more complicated routines (.py script files).
by "rotate the system" do you mean a movie-like 360° rotation? Then your simple list of PyMOL commands will be something like:
Sure you can do some sophisticated stuff but you don't have to. All my files will be simple atom list in xyz format (name \t x \t y \t z), and all I want to do is select all the atoms of a certain name, color them and then rotate the system.
# color everything gray and histidines blue
color gray, all
color blue, resn HIS
# make 100 movie frames and do full rotation about Y-axis
mset 1 x100
For documentation and more examples see:
MPI for Developmental Biology
My other email account has a "professional" signature.