VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 19 2019 - 10:53:26 CDT

Hi,
  I realized, I forgot to mention another scene format that is rapidly
becoming interesting. Pixar's "USD" format supports a bunch of
sophisticated geometric primitive types, but it's still relatively
heavily geared toward triangle meshes. A key interest in USD however
is that it is designed to be extensible, and there are a large number
of companies implementing tools that import/export scenes in USD format.
I haven't started writing a USD exporter for VMD yet as I have to
come to grips with all of the associated library dependencies and
complexity that they would add to the VMD compilation process,
but it looks like there's a great deal of future potential there.

Pixar and other contributors have made all of the USD source code, test
cases, and even full-up example renderers freely available as open source IIRC,
so there's an impressive foundation for tools like VMD to build on:
  https://graphics.pixar.com/usd/docs/index.html

If/when I have some prototypical USD support in a public version of
VMD I'll definitely make people aware of it.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Sep 19, 2019 at 10:43:17AM -0500, John Stone wrote:
> Hi,
> Aside from the workaround and I described to Walter, OBJ is a very poor
> choice for these kinds of scenes as it doesn't even support per-vertex colors.
>
> Also, while OBJ does (in its original form) support spheres and cylinders,
> almost none of the existing open source software tools (Blender et al.)
> are capable of parsing anything other than triangle mesh geometry,
> so VMD only uses the subset of the OBJ format geometry types that
> these other tools can actually parse. I would generally advise people
> to use more modern scene formats such as X3D whenever possible.
>
> I've been working with the Khronos glTF group to convince them to add
> support for spheres, cylinders, and other geometry types that are critically
> important for molecular visualization, but it will have to happen in future
> versions of the glTF spec.
>
> My hope is that we'll get an increasing fraction of what we need in future
> revs of glTF and X3D which are both actively under development.
>
> Best,
> John Stone
>
> On Thu, Sep 19, 2019 at 07:37:07AM +0000, Luciano Abriata wrote:
> > Ciao Walter,
> >
> > I've been using obj+mtl files for some AR applications and indeed, the colour information of some objects, particularly meshes, is lost. Luckily, in HTML you can color-code the mesh ad hoc (this only works if you don't load the mtl file, thus leaving all materials free to be set from code). Maybe you can use a similar trick in the program you are using.
> >
> > Note I have also seen some inversions going on in the meshes (like say x coordinates become -x) that I don't understand, but luckily HTML provides a way to re-invert them. I asked about these issues in this mailing list but apparently there's not much development going on.
> >
> > Best
> >
> > Luciano
> >
> > ________________________________________
> > De: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] en nombre de Walter Rocchia [Walter.Rocchia_at_iit.it]
> > Enviado: miércoles, 18 de septiembre de 2019 23:10
> > Para: vmd-l_at_ks.uiuc.edu
> > Asunto: vmd-l: exporting 3D model of a volume-based colored mesh
> >
> > Hi,
> > I would like to export the mesh of a surface created in VMD and colored based on a electrostatic potential. The final aim would be to have a 3D model on it (e.g. a .u3d format)
> > I tried most of the output options provided by VMD, including wavefront .obj and .mtl files. When the surface is colored with a colorID, it seems to work.
> > In contrast, when I loaded these files in Meshlab, it seemed that the information of the color was missing?
> >
> > Is there any way to do it correctly?
> >
> > Thank you
> > Walter
> >
> > *********************************************************************
> > Walter Rocchia, PhD, Head
> > Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab<https://urldefense.proofpoint.com/v2/url?u=https-3A__concept.iit.it&d=DwMGaQ&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=JBqQLS7jZ5whrB0hXJY8MNYcfDrh8UhlGJ2ANxoi8s0&m=IMSOYQxDteyG_ge_qxjPTnX6-k5PSRM7WnsmiyXyAMI&s=H8w19ltzEsfSzCdd6zsxnB8g8xUhmMkVGiCELWlagcw&e=>
> > ISTITUTO ITALIANO DI TECNOLOGIA
> > Via Melen ? 83, B Block, 16152 - Genova, Italy
> > Phone: +39 010 2897418
> >
>
> --
> NIH Center 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/ 

-- 
NIH Center 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/