Dear Kristian, Warren, and other Pymolers:
In regard to my previously stated problems in making movement animations in
Pymol, I have tried the rTools plug-in before, and I tried it again after
your suggestion. In my system they do not work correctly, or at least I
have not installed them correctly. I am running both a Mac powerbook and a
G4 desktop machine, with either the stand-alone Pymol 10.2 for Mac OSX or
Pymol version 0.86 running in unix in the Mac X11 version of the X windows
system. As indicated in the install instructions for rTools (version0.5.2) I
have copied the rubor.py and rubor/ directory into the
.../modules/pmg_tk/startup directory, modified the path in rConfig.py,
created /tmp and /pdb directories (in the startup directory because the
install instructions were not clear on this topic), added the relevant lines
to PMGApp.py. I should state that several aspects of the install
instructions in regard to the directory structures in my system were
unclear.
In both versions of Pymol described above, when a simple move command is
inserted into a script as follows:
mset 1 x100
mvMove 20-40,x,80
movie
I get the following error messages:
PyMOLmset 1 x100
PyMOLmvMove 20-40,x,80
Traceback (most recent call last):
File /Applications/PyMOL/Darwin/modules/pymol/parser.py, line 234, in
pars
e
exec(com2[nest],pymol_names,pymol_names)
File string, line 1
mvMove 20-40,x,80
^
SyntaxError: invalid syntax
PyMOLmovie
Error: ambiguous command:
movie.loadmovie.rockmovie.screw movie.zoom
movie.nutate movie.rollmovie.tdroll
Obviously I have made a mistake in the install process somewhere, and I
would appreciate a more detailed description of where and why the plug-in
components are supposed to be inserted since I will have to interpret them
for my own directory structure rather than a standard Linux install.
Regardless of all of the above, there also MUST be an easier way to do the
animations that I need. Is there no direct scripting in Pymol that can do
the equivalent smooth moves or transitions? The rTools package may be the
way to go in the future, especially if it in incorporated in a seemless
manner into the next version of Pymol that works in ALL platforms without
undue tinkering with scripts and directory structures. In the meantime is
there an effective Pymol scripting approach that will work in the platforms
that I have described above?
Any assistance would be greatly appreciated.
Regards,
Kelley
On 4/1/03 4:43 AM, Kristian Rother kristian.rot...@charite.de wrote:
Am Montag, 31. März 2003 23:18 schrieb Kelley Moremen:
Dear Pymolers:
The problem comes when I want to make defined rolls, zooms, or moves that
start and stop at specific places. There must be a better way than
concatenating a collection of move x,10 commands. I have seen in several
There is a plug-in for PyMOL on http://www.rubor.de/bioinf/ that has been
designed to handle that kind of thing. With it installed, you can do the
following:
mvMove 1-100,z,50# Zoom over frames 1-100
mvRot 50-110,x,260 # Rotate around x-axis
mvSet 1-10,transparency,1.0,0.0 # fade surface in
movie# start the whole thing
Maybe that helps,
Kristian Rother
Dr. Kelley Moremen
Associate Professor
Complex Carbohydrate Research Center
Department of Biochemistry and Molecular Biology
University of Georgia, Athens, GA 30602-7229
Office (706) 542-1705Fax: (706) 542-1759
Email: more...@arches.uga.edu
(send email with large attachments to: more...@bmb.uga.edu)
Website: http://bmbiris.bmb.uga.edu/moremen/lab/
