VMD-L Mailing List

From: Sergio Decherchi (sergio.decherchi_at_iit.it)
Date: Sat Jan 28 2012 - 14:22:10 CST

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