VMD-L Mailing List

From: Daniel Strahs (dstrahs_at_fsmail.pace.edu)
Date: Sun Sep 18 2005 - 18:39:00 CDT

John:

My intention in asking this question is to supplement the support currently missing for mapping APBS potentials on surfaces in MesaGL VMD installations.

If the atom IDs could be used to identify the surface elements (and their associated facets/vertices), then I could write a script that identified the electrostatic potential located near the facet/vertex point, and directly color that facet/vertex point based on the caretesian coordinates of the surface element.

As it is, my only option seems to be to map the average electrostatic potential on the atoms beta or occupancy values. This offends my intention of accurate scientific representations: it is well known that points sampled within the atomic radii have artifactual potentials. In my past uses with Delphi, I have been quite aware of the artifacts in anomalously unphysical potential positions (created by averaging grid positions onto individual atoms). Programs such as phitopdb propagate these artifacts.

Ideally, to approximate the visualization of the electrostatic potential located at the molecular/accessible surface, I would need to consider only those EP grid points located at the grid elements corresponding to the surface. To account for this, I have to run a second MSMS/Surf solely to identify the facet/vertex locations. I can get the commands for the MSMS/Surf surface from "graphics get top". Once I prepare the second surface file and identify the vertex elements, I then need to locate the grid points corresponding to the vertex elements. From there, I can select which grid potentials to average onto the surface atom that they're closest to; from there, I can then color the surface by the average of the grid points corresponding to the associated surface locations (placed in the cognate atoms occupancy/beta).

As you can see, this is a complicated script: one that I will nonetheless be happy to write rather than dealing with the artifacts inherent in potsurf.tcl.

Since there is currently no tag used to select the surface elements associated with an atom, I would like to suggest that such a feature be made available for a future VMD version.

Dan Strahs

---------- Original Message ----------------------------------
From: John Stone <johns_at_ks.uiuc.edu>
Date: Fri, 16 Sep 2005 21:03:41 -0500

>
>Dan,
> The way that Surf and MSMS operate, each triangle facet or vertex
>(facet for Surf, vertex for MSMS) is associated with a particular atom.
>Once loaded into VMD, these surfaces are colored based on the atom they
>are associated with. There's no way to directly access the mesh data nor
>the atom tags associated with the surface from the atom selection language
>at this time. What are you interested in doing with the atom tags and/or
>surface data?
>
> John Stone
> vmd_at_ks.uiuc.edu
>
>On Fri, Sep 16, 2005 at 08:44:53PM -0400, Dan Strahs wrote:
>>
>> Hello all:
>>
>> Surfaces generated with MSMS and SASA are associated with tags that
>> identify the atoms to which these surfaces belong.
>>
>> So some questions:
>>
>> 1) Is every surface element associated with only one atom?
>> 2) Are there keywords to access the surface elements for a given
>> atom selection?
>>
>> Thanks!
>>
>> Dan Strahs
>
>--
>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
>

 

 
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