VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 19 2005 - 10:19:59 CDT

Daniel,
  At this point I'd be surprised if there are people actually using Mesa
intentionally, except those who have video boards that are hopelessly
unsupported by Linux or something of that nature. You have to admit that
trying to work around the lack of 3-D texture mapping is painful. I considered
implementing the feature you're interested in previously, but decided that
the neverending march of progress with graphics accelerators essentially
gaurantees that everyone will have hardware accelerated 3-D texture mapping
shortly and that it wasn't worth my time to try and do without it. The main
short-term problem with my decision is that most of the software renderers
(POV-Ray, etc) still don't do 3-D texture mapping and some of the OpenGL
drivers out there (Apple) have 3-D texturing bugs the make it unusable at
the moment. I concede that it would be nice to have a fallback rendering
path that used simple Gouraud shaded triangles when 3-D texturing is
unavailable, or subject to buggy drivers. I'll consider adding this to
a subsequent version of VMD. For various reasons however it's not practical
for me to add atom selection commands for components of the surface meshes
generated by MSMS/Surf at this time. At present, there's actually no user
access to internal surface mesh data of this sort. In the short term,
the only real way to deal with this would be to write a script that generates
the surface with MSMS/Surf, and and builds a surface with the draw commands.
I'll have to think about how practical it would be to add a
fallback rendering path for vertex-colored surfaces from volume data.
Unlike the 3-D texturing code which applies to all representations, it would
only be reasonable to do this for certain molecular representations such
as Surf/MSMS, and maybe the NewRibbons and NewCartoon.

  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Sep 18, 2005 at 07:39:00PM -0400, Daniel Strahs wrote:
> 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
> >
>
>
>
>
>
>
>
> _______________________________________________________________________
> Sent via Pace University's WebMail system at fsmail.pace.edu
>
>
> 

-- 
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