VMD-L Mailing List

From: Sergio Decherchi (sergio.decherchi_at_iit.it)
Date: Thu Feb 02 2012 - 02:59:49 CST

Hi,
Thank you John. I'll begin playing with VMD code in order to add my
surfaces support and to do some trials.
I think that I will simply load a previously generated surface because
the execution time, at this development stage,
can be non interactive.
Thanks,
sd

Il 01/02/2012 23:21, John Stone ha scritto:
> 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