VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 23 2005 - 17:03:03 CDT

Nicolas,
  Glad you got it all working. Even "simple" scripts can be complicated
to debug now and then.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Sep 23, 2005 at 06:44:57PM +0200, Nicolas Sapay wrote:
> John,
> Thanks for your advices. I have found a problem. For some reason, I use
> several VMD configuration file that I load as a function of what I want
> to do. And of course, I have redefined the white color in light grey in
> one of them. So, mea maxima culpa. That will teach me to have tens of
> configuration file :-)
>
> Nicolas
>
> Le ven 23/09/2005 à 17:29, John Stone a écrit :
> >
> > Nicolas,
> > This is very strange, I get a perfectly white background when I
> > do the same thing. Are you re-defining any of the VMD colors when you
> > run the rendering job? The code that emits the background color for
> > Tachyon, POV-Ray, and Raster3D is implemented exactly the same way, so
> > I'm not sure how you could be getting different colors. Can you send
> > me the structure(s) and scripts or saved states that you're using to
> > render the images so I can try to reproduce this problem locally?
> > When I do this by hand it works perfectly so there must be something
> > different about what you and I are doing. If you can send me the necessary
> > files/data to reproduce what you're doing, I should be able to solve the
> > problem for you one way or another.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> > On Fri, Sep 23, 2005 at 05:21:38PM +0200, Nicolas Sapay wrote:
> > > John,
> > > That is exactly what I do in my script (sorry, my previous message was
> > > not clear):
> > > color Display Background white
> > > and then I render the picture:
> > > render Tachyon foo.dat
> > > and I run Tachyon
> > > tachyon foo.dat -aasamples 4 -trans_vmd -fullshade -format TARGA -o
> > > foo.tga
> > >
> > > So, when I use Raster3D, the background is indeed white in the rendered
> > > picture. But it becomes gray with Tachyon, TachyonInternal or POVray.
> > >
> > > Nicolas
> > >
> > > Le ven 23/09/2005 à 16:50, John Stone a écrit :
> > > >
> > > > Nicolas,
> > > > Before you use the "render" command in VMD, you'll want to redefine
> > > > the background color in VMD so you don't have to edit the output produced
> > > > by Tachyon or POV-Ray. To do this you'd use a command like this:
> > > > color Display Background iceblue
> > > >
> > > > Let us know if you need more help with this.
> > > >
> > > > John Stone
> > > > vmd_at_ks.uiuc.edu
> > > >
> > > > On Fri, Sep 23, 2005 at 02:20:07PM +0200, Nicolas Sapay wrote:
> > > > > hello everybody,
> > > > >
> > > > > I am trying to render VMD scene in batch mode trough TCL script with a
> > > > > white background. When I use Raster3D, all is OK. But, when I use
> > > > > Tachyon or POVray, the background becomes gray. In fact the background
> > > > > is indeed set to gray (RGB 0.9, 0.9, 0.9) in scene files (*.dat/*.pov).
> > > > > How can I solve this problem? Of course I can use "tr" or "awk" to
> > > > > translate the wrong Tachyon/POVray line in batch mode, but I am not sure
> > > > > it is really tricky.
> > > > >
> > > > > Cheers
> > > > >
> > > > > Nicolas
> > > > > --
> > > > > _ Nicolas Sapay ____________________________________________
> > > > > Ph.D sudent in structural bioinformatics
> > > > > Institut de Biologie et Chimie des Proteines
> > > > > CNRS - Claude Bernard University, IFR128 Bioscience Lyon-Gerland
> > > > > 7, Passage du Vercors Tel: +33 (0)4 72 72 26 46
> > > > > 69367-F Lyon cedex 07 Fax: +33 (0)4 72 72 26 04
> > > > > France Web: http://pbil.ibcp.fr/
> > > >
> > > > --
> > > > 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
> > > --
> > > _ Nicolas Sapay ____________________________________________
> > > Ph.D sudent in structural bioinformatics
> > > Institut de Biologie et Chimie des Proteines
> > > CNRS - Claude Bernard University, IFR128 Bioscience Lyon-Gerland
> > > 7, Passage du Vercors Tel: +33 (0)4 72 72 26 46
> > > 69367-F Lyon cedex 07 Fax: +33 (0)4 72 72 26 04
> > > France Web: http://pbil.ibcp.fr/
> > >
> >
> > --
> > 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
> --
> _ Nicolas Sapay ____________________________________________
> Ph.D sudent in structural bioinformatics
> Institut de Biologie et Chimie des Proteines
> CNRS - Claude Bernard University, IFR128 Bioscience Lyon-Gerland
> 7, Passage du Vercors Tel: +33 (0)4 72 72 26 46
> 69367-F Lyon cedex 07 Fax: +33 (0)4 72 72 26 04
> France Web: http://pbil.ibcp.fr/
> 

-- 
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