VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 01 2012 - 16:21:39 CST

Sergio,
  If you're writing your own surface mesh generation tool, it may be
simpler to create a new VMD representation for your tool than to try
and support the volumetric coloring on arbitrary meshes. It would not
be hard for you to start with the code in the DrawMolItemMSMS, or
DrawMolItemQuickSurf and modify it to either call your program to
compute the surface mesh, or to read an appropriate mesh file as-needed.
This would be a simple way to let you prototype something. If your
mesh generation program isn't fast enough for interactive calculations
(e.g. slower than Surf or MSMS) then we should talk about this further
and I'll see if there's a good way to add arbitrary mesh support in some
way, soon enough to benefit your work. Let me know what you think.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Jan 28, 2012 at 09:22:10PM +0100, Sergio Decherchi wrote:
>
> Hi,
> thanks. What is the name of the temporary .vert and .face files that are
> produced when running MSMS from VMD?
>
> I am developing a software able to build/analyze both molecular surfaces
> and arbitrary mesh surfaces.
> I would like to see them on VMD together with a surface potential map .
> The output meshes are in .off
> format and can represent any surface; for now I only have triangles and
> vertices info in the file without normals.
> Then, using a python script the .off file is converted into MSMS by
> estimating vertex normals such that I can see the surface on VMD; the
> other info
> in the file is dummy (one may not have a notion either of patch or of
> atom).
> The 'mesh' generic representation would be very useful in order to see
> the potential but may be not necessary: I suppose it is sufficient
> to enable the volume colouring when a .off file is loaded by the .off
> plugin. Does the .off plugin require vertex normals for correctly
> displaying the surface? If I am able
> to load an .off file (may be necessary to write the normals?) then the
> suggested modification should be sufficient.
> Cheers,
> sd
>
> Il 28/01/2012 17:38, John Stone ha scritto:
> >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
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