> 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 >
