VMD-L Mailing List

From: Jim Fonseca (jf163201_at_ohiou.edu)
Date: Tue Apr 03 2007 - 15:38:41 CDT

Thanks! That worked great.

Jim
On Apr 3, 2007, at 1:31 PM, John Stone wrote:

>
> 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