VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 02 2006 - 13:05:12 CDT

Hi,
  For cavities and pores, you could try using the new volumetric map
generation plugin, found in the Extensions->Analysis->VolMap Tool menu
in the main VMD window. (requires VMD 1.8.4, not available in older versions)
To display cavities or pores you'd generate a density or occupancy map,
and then display the map with an isosurface with a isovalue of zero,
or a near-zero value to show the regions not containing atoms. Much would
depend on the details of your structure of course, but it should be possible
to do this with the built-in VolMap tool, or by using the 'volmap'
text command if the graphical tool doesn't afford enough control for
your purposes.
  http://www.ks.uiuc.edu/Research/vmd/plugins/volmapgui/

The previously most common way of displaying pores in VMD was via
the HOLE program by Oliver Smart, and load the resulting sphere set into
VMD with an example script for this purpose in the VMD script library.
The HOLE program and scripts work with older versions of VMD as well as
the latest version.

Dr. Smart's home page (contact him to get HOLE):
  http://www.globalphasing.com/people/osmart/

VMD hole script:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/hole/

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, May 02, 2006 at 12:50:38PM -0600, Wei Fu (Linda) wrote:
> Hello,
>
> Is there any way to display the volume of cavity/pocket/channel of a protein in VMD? Do I need to install some plugin program or calculate the volume of cavity by other software, then use VMD to read the map of the volume?
>
> Best,
>
> Linda
>
> 2006-05-02
>
> Linda
> Postdoctoral Research Associate
> Department of Biology and Biochemistry
> University of Houston
> 4800 Calhoun Rd. HSC #402C
> Houston, TX 77204-5001 USA
> Phone:713-743-8355(o)
> Fax:713-743-8351
> Email: fuwei_at_adrik.bchs.uh.edu
> http://adrik.bchs.uh.edu/~fuwei/
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078