Hi Tom,
I guess the first part of your question has already been answered pretty
well. If you want to go down the path of the 3d modelling software, I think
your best option is molecular Maya, which you can find on
www.molecularmovies.com. You'll also find tutorials there.
Cheers,
Simon
On 5/1
Hi Robert,
PyMOL>help rotate
DESCRIPTION
"rotate" can be used to rotate the atomic coordinates of a
molecular object. Behavior differs depending on whether or not the
"object" parameter is specified.
So much for rotate. The help for turn is misleading:
PyMOL>help turn
DESCRIPTI
Dear Robert,
I downloaded the msms 2.6.1 from
http://mgltools.scripps.edu/downloads#msms and
installed into C:\Program Files\MSMS. But there are still something wrong
after running the script:
There seems to be a problem with the msms output
Traceback (most recent call last):
File "C:\Program
You can solve it by adding the following line in the msms_pymol.py you
downloaded from Robert's page to line 133, right before msms_cmd is defined.
if msms_path.startswith('C:/'): msms_path = '\"%s\"' % (msms_path,)
Basically, your problem was caused by the whitespace in the path to the
MS
Hi all,
PyMOL allows for both camera and object coordinate changes. When you
use the mouse to move stuff around, that's the camera moving*--just
like the 'turn' command. When you use "rotate", object dragging or
some of the other matrix transformation commands (fit, super, align,
matrix_copy, up
Peter,
If you knew the positions of the end points of the lines you could
make CGO lines, or you could just use a distance measure between two
pseudoatoms and modify some label/dash settings:
# make two new pseudoatoms, just for
# making a distance measure between them
# Specify your own position
Hi Hongbo,
On Wed, 12 May 2010 15:59:36 +0200 Hongbo Zhu
wrote:
> You can solve it by adding the following line in the msms_pymol.py you
> downloaded from Robert's page to line 133, right before msms_cmd is defined.
>
> if msms_path.startswith('C:/'): msms_path = '\"%s\"' % (msms_path,)
>
Hi Peter,
On Wed, 12 May 2010 10:42:36 -0400 Jason Vertrees
wrote:
> Peter,
>
> If you knew the positions of the end points of the lines you could
> make CGO lines, or you could just use a distance measure between two
> pseudoatoms and modify some label/dash settings:
As Jason says, if you hav
Hi Jason,
Well, this is just polemic... But anyway. If I export the scene to
povray, the camera will always be placed at the origin. If I then want
to add something to the scene that is defined in the original
coordinates of the pdb file, I have to apply the transformation
encoded in the matrix ob
Hi,
One of my users is getting this:
PyMOL(TM) Incentive Product - PyMOL Executable Build
Copyright (C) 2009-2010 Schrodinger, LLC
This PyMOL Executable Build is available only to PyMOL Power, Casual, and
Developer Users who have a valid license to use this software product. Any
other usa
Tom-
Take a look at slerpy: http://pymolwiki.org/index.php/Slerpy
It was written to do exactly what you describe...and of course it is the
camera that moves. The coordinates of the molecule are not changed
unless you go into edit mode.
Best,
Joel
-Original Message-
From: Dupree Tom [
Hi Ben,
A couple things come to mind:
(1) Always use the latest "proven" NVidia drivers; 180.xx is not current.
(2) Some RH versions use Tcl/Tk 8.4 over 8.5. Which is yours using?
(3) Could you please send me the md5 sum for your copy? We should
make sure it's not corrupted.
Cheers,
-- Jason
Thank you everyone for giving me your time,
I think I failed to explain what I am trying to do correctly/clearly...or I
simply do not understand your answers, either is possible :)
What I really want is to be able to explore binding sites from inside the
binding site.
Take a room with a couch
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