VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 11 2006 - 16:18:23 CDT

Ralph,
  The scene export code in VMD uses various different strategies depending
on the limitations of the file format we're exporting to. Some file formats
don't have any support for spheres, cylinders, triangle strips or
vertex arrays, and others have them, but require color and material
information to be specified at every vertex, which can fatten up the
exported files tremendously.

When we have to emit spheres and cylinders as triangles, that by itself can
make the exported scene very large. Going beyond that however,
I would say that it's often the color and material information that is
the direct cause of file bloat with the old scene file formats. I have
no idea how sophisticated these Blender input filter Python scripts are,
but I have a feeling that many of them probably only work with the simplest
form of some of these formats. VRML is a good example of a format that
is pretty easy to write but very difficult import due to the huge diversity
of options that may be difficult to support. I suspect that this is what's
going on with some of the formats you've tried importing into Blender.
I believe our Wavefront export doesn't include material data presently,
so that may be one that would work well with Blender with a bit more work.

  John

On Tue, Jul 11, 2006 at 01:19:30PM -0600, Ralph Jimenez wrote:
> John,
> Of the formats that VMD offers, only STL, Wavefront and VRML 1.0 can
> be imported by Blender's standard import filters.
> The VRML input sometimes does not work in Blender, and usually only
> creates a mesh that is unusable.
> Wavefront and STL do work, but all information on the materials and
> lighting are lost on import...this problem might be due to Blender's
> import filter.
> With a small protein, 100 residues and cofactor, displaying the
> backbone as a cartoon and a few sidechains and cofactor as licorice, the
> resolution should be set very low (<50) in which case the STL or OBJ
> files are still ~ 100 MB. VMD seems to output quite a few redundant
> vertices/edges, and internal points that make the mesh much larger than
> necessary. I suspect this issue has to do with the way that VMD exports
> the mesh...
> Anyway, it would be great to see the two programs work nicely
> together. I'm still learning to use Blender, but the potential is
> impressive!
> Ralph
>
>
> John Stone wrote:
> >Hi,
> > From what I understand, the native Blender .blend file format is
> >very version specific, changes with every release, and people suggest
> >you not use it directly. STL is not an appropriate format to use to
> >import VMD scenes into Blender as you've discovered, it's meant to be
> >used for Stereolithography, but not much else. What other formats have
> >you tried importing into Blender? If you know of a file format that
> >Blender supports well, I'd certainly consider writing an export module
> >for VMD to better support it. I would have expected Wavefront OBJ
> >or one of the VRML formats work ok with Blender already.
> >
> >Here's a discussion of why the .blend file format isn't documented etc:
> > http://www.blender.org/forum/viewtopic.php?t=8143&sid=ced5749c0154f65b37501dd929205166
> >
> >There is now a "BlendXML" development effort in progress to make a Blender
> >scene file format that's usable by other software, but as far as I can tell
> >it's far from finished.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> >On Tue, Jul 11, 2006 at 09:32:31AM -0600, Ralph Jimenez wrote:
> >>It would be great to use VMD's output with an open-source 3D
> >>modelling/animation program like Blender (www.blender.org). This program
> >>can be used to make some fantastic images and animations, output video
> >>files, etc. It would make a nice combination with VMD.
> >> I've been able to read .STL files into blender, but the other formats
> >>do not work very well. Even with STL, the lights are not imported, and
> >>the molecule is imported as one mesh object- no separate
> >>cofactor/protein, for example. So my feature request is for VMD to write
> >>Blender scene files...
> >> I'm curious...has anyone else tried using Blender with VMD?
> >>
> >>--
> >>Ralph Jimenez, Ph.D.
> >>JILA/NIST and Department of Chemistry & Biochemistry
> >>440 UCB
> >>University of Colorado, Boulder
> >>Boulder, CO 80309-0440
> >>
> >>Tel: (303) 492-8439
> >>FAX: (303) 492-5235
> >>
> >>http://jilawww.colorado.edu/JimenezLab
> >
>
>
> --
> Ralph Jimenez, Ph.D.
> JILA and Department of Chemistry & Biochemistry
> 440 UCB
> University of Colorado, Boulder
> Boulder, CO 80309-0440
>
> Tel: (303) 492-8439
> FAX: (303) 492-5235
>
> http://jilawww.colorado.edu/JimenezLab/ 

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