VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 24 2014 - 10:19:22 CDT

Darrell,
  If you can provide a gzip/zip file that contains your GAMESS log file
and an associated VMD saved state that loads it in the form you want to
export to .obj, I would be happy to take a look at what may be
going on in this case.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jul 24, 2014 at 11:00:20AM -0400, Darrell Kuykendall wrote:
> Hi,
>
> Yes. Running VMD 1.9.1 on Mavericks. I'm loading GAMESS .log files into VMD and using orbital representations, then rendering as .obj to move over to Maya.
>
> This afternoon, I'll be doing more testing and will post any discoveries.
>
> Thanks!
> Darrell
>
> > On Jul 24, 2014, at 10:37 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > 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/ 

-- 
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/