VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 03 2007 - 12:31:16 CDT

Jim,
  Rather than using Surf or MSMS to calculate a solvent surface
for this structure, I'd suggest using the VolMap plugin to calculate
a density map synthesized from your atom coordinates. Surf and MSMS
both calculate solvent surfaces, and as such they expect the structure
not to have many atoms inhabiting the same space, nor to have atoms with
unusually large radii etc. Fortunately, the VolMap plugin in VMD should
be far more tolerant of these properties of your artificial structure.
I would expect it to generate a synthetic density map without problems.
The VolMap plugin is included in the "analysis" submenu of the VMD
Extensions menu. Check out the online help here:
  http://www.ks.uiuc.edu/Research/vmd/plugins/volmapgui/

Once you've created a synthetic density map from your structure, you
can use the VMD Isosurface representation to render it.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 03, 2007 at 12:25:49PM -0400, Jim Fonseca wrote:
> Hi,
> I'm trying to show a surface of a series of atoms with artificial
> radii. It's supposed to represent a permeation pathway where the
> atoms are located along the pathway and the radius of each atom
> indicates the radius of the pathway. The pdb format is:
> MODEL 0
> ATOM 1 P TUN 0 71.454 59.394 75.674 0.86 0.00
> ATOM 2 P TUN 0 72.154 59.394 75.674 1.46 0.00
> ...
> ENDMDL
>
> The radius of each atom is saved in the occupancy field of the pdb
> file, so I load this data into the radius using $sel set radius.
> This seems to work as the VDW representation shows the atoms with the
> appropriate radii.
>
> However, when I try to show a surface representation I get the
> following:
>
> Reading 82 atoms..done
> Probe radius = 1.400
> Constructing solvent-accessible surface ..
> Max edge length = 1.200
> unusual malloc(0)
> unusual malloc(0)
> Atom density > MAX_DENSITY
> Info) Reading Surf geometry output file...
> Info) Read Surf output file, processing geometry...
> Info) Done.
>
>
> Some of the radii become quite large (~10 Angstroms). Seems like too
> many overlapping atoms have made the atom density too large, but I
> have no idea how to get around this. I'd really appreciate any
> suggestions on how to show this with the surface representation.
>
> Thanks!
> Jim Fonseca 

-- 
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