VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Jan 28 2012 - 10:38:49 CST

Hi,
  With the existing code, you could trick VMD into reading the MSMS
.vert and .face files into an MSMS representation by using a fake
"msms" binary that provides your mesh files instead of something
produced by the real MSMS program. If you're willing to wait until
after I get VMD 1.9.1 released, I could also add an experimental
"mesh" representation that would let you load the mesh via your
plugins, and display it in VMD and apply volumetric coloring to it.
Just out of curiosity, where are the meshes that you're generating
coming from? Most likely there might be a better way of doing this
if I know more about what program is producing your meshes and what
properties they have or don't have. Do you associate atom indices
with your mesh vertices?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Jan 28, 2012 at 12:57:10PM +0100, Sergio Decherchi wrote:
>
> Hi,
> thanks. I asked that because I wrote a converter from arbitrary .off meshes
> to msms files to load virtually any mesh on VMD. I already tried loading
> .off files directly but it didn't work.
> My goal is to see the surface potential on arbitrary surfaces that I can
> load as a msms file.
> Can VMD be modified in that direction? Or, is there already a way to see
> a surface potential on an aribitrary mesh surface?
> Thanks,
> sd
>
> Il 27/01/2012 22:39, John Stone ha scritto:
> >Hi,
> > Try computing the MSMS surface inside of VMD, and that should cure
> >your problem. Surfaces loaded from external files are treated as
> >raw graphics and are not modifiable (e.g. color by volume) like
> >VMD's internal representations are, so in order to color by volume,
> >you should have VMD perform the MSMS computation internally.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Fri, Jan 27, 2012 at 06:52:12PM +0100, Sergio Decherchi wrote:
> >>Hi,
> >>I would like to colour with the potential (from DelPhi) the surface of
> >>an externally loaded msms file.
> >>I tried first by loading the msms file and the potential file
> >>separately; then I tried by embedding into the msms surface
> >>the potential but in both cases I was not able to see the potential on
> >>the surface by using volume colouring.
> >>Also I was not able to make transparent the externally loaded msms
> >>surface.
> >>Any suggestion?
> >>Thanks,
> >>sd 

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