> From: Mirek Cygler [mailto:mirek.cyg...@bri.nrc.ca]
>
> I am trying my first steps with PyMOL. I have tried to
> display a XPLOR map.
> It worked well but the isomesh command displayed the entire
> map. How can I
> display only a part of the map (box or sphere) around a
> specific point (say,
> the center of the screen) if I do not have a model yet (ie, no atoms).
Mirek,
That exactly functionality isn't yet implemented, but you can kludge
it by:
1. creating a model on the fly
2. setting the atom coordinates in the model to the location
3. creating a mesh around the model
4. and deleting the model.
The following .pml example script shows you how to get a 10 A brick
(msh1) or a sphere (msh2) about (2.0,21.0,4.0). If you plan to use this
functionality often, you should convert the following script into a
Python function with four arguments and place its definition in your
PyMOL start-up file. This is how you can customize PyMOL to suit your
needs...
# begin example
fragment methane,_pos
alter_state 1,(_pos),x=2.0;y=21.0;z=4.0
isomesh msh1,map1,1.0,(_pos),10.0
isomesh msh2,map1,1.0,(_pos),carve=10.0
del _pos
zoom msh1
# end example
Cheers,
Warren
cc: PyMOL mailing list
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 fax: (650)-266-3501
>
