On Tue, 18 Apr 2006, Chun Tang wrote:
Dear PyMoler,
In the pymol apbs tool, there is an option to show the
negative/positive isosurface (not the molecular surface) upon loading
an electrostatic map. My question is if there is a way to show the
electrostatic potential surface as mesh instead of solid surface, also
if it is possible to show the potential as a series of contours. Thank
you.
Chun
The plugin doesn't allow you to show a mesh, but it would be a good idea
to build that in. You can do it from the command line with the isomesh
command. If you're using the plugin to do everything, you can do
something like this:
isomesh iso_pos_mesh, apbs_map, 0.5
color blue, iso_pos_mesh
If you're not using the plugin, change 'apbs_map' to whatever your map is
called.
the idea of showing a series of contours is probably a good one. I'm not
sure how to make a nice GUI interface for it, though.
I recently switched to a Mac. It was broken for quite a while, but I
think I finally got things working properly this weekend. I'll try to put
out a new version of the plugin soon. At the moment, here's what I'm
planning to add:
- the ability to use pdb2pqr to generate pqr files
- the ability to display the APBS version
- the ability to display isomeshes in addition to isosurfaces
any other big suggestions?
-michael
--
www.umich.edu/~mlerner | _ |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan
it's a cheer-ocracy. | - against HTML email X | Biophysics
-Torrence, Bring It On| / \ | mler...@umich
-------------------------------------------------------
This SF.Net email is sponsored by xPML, a groundbreaking scripting language
that extends applications into web and mobile media. Attend the live webcast
and join the prime developer group breaking into this new coding territory!
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642
_______________________________________________
PyMOL-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/pymol-users
