VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 24 2014 - 09:37:08 CDT

Hi,
  Which version of VMD are you running presently? I'm guessing 1.9.1 based
on the .mtl comment below.

How are you rendering the orbitals, what file format(s) are you loading,
and are you rendering a density map using an isosurface representation in
VMD, or are you using the Orbital representation in concert with a GAMESS
or Molden input file?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jul 23, 2014 at 04:30:19PM -0400, Darrell Kuykendall wrote:
> Hi, all,
> I*ve been using VMD to create .obj files (among other things) for ab
> initio structures, which I then bring into Maya for animation. All has
> worked well until recently when I*ve begun to render orbitals as well. One
> phase of an orbital always renders as a *transparent* or *ghosted*
> material. I use quotes because no matter what material is assigned to this
> object it remains transparent. Interestingly, if I do certain spatial
> transformations in Maya, the object appears as expected (not transparent)
> but as soon as it is placed back at its intended position, it goes
> transparent again.
> In the limited amount of troubleshooting I was able to do this afternoon,
> I discovered that: 1) exporting only the properly rendered phase of a
> symmetrical orbital as .obj from VMD and then copying and reflecting this
> orbital in Maya works until the copy is in an exact mirror position, then
> it becomes transparent and 2) there doesn*t seem to be any correlation
> between the order of representation creation in VMD and which orbital gets
> affected, nor the phase.
> I*ll keep playing around to see what else I can discover. Incidentally, I
> saw that the mtllib statement in the .obj files from VMD incorrectly
> reference the associated .mtl (first letter of .mtl filename is always
> missing). I can see reasons that that might be intentional though.
> Thanks for any help!
> D 

-- 
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/