Great, thank you.

On Mon, Sep 12, 2011 at 10:05 AM, Thomas Holder <speleo3@users.sourceforge.net> wrote:
Hi Yotam,


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.

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.

The other language is pure python (PyMOL API) and can be used to write more complicated routines (.py script files).

http://pymolwiki.org/index.php/Running_Scripts


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.

by "rotate the system" do you mean a movie-like 360° rotation? Then your simple list of PyMOL commands will be something like:

# 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
util.mroll
mplay

For documentation and more examples see:
http://pymolwiki.org/index.php/Color
http://pymolwiki.org/index.php/Util.mroll
http://pymolwiki.org/index.php/Property_Selectors
http://pymolwiki.org/index.php/Selection_Algebra

Cheers,
 Thomas

--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen



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