VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 06 2003 - 10:51:46 CST

Hi,

On Wed, Feb 05, 2003 at 05:48:33PM -0800, Margaret Cheung wrote:
>
> Dear John,
> Thank you! I'm still having troubles, and yes, I have not used Rayshade
> before. (I don't even know how to view it after saving it in winxp).

Ah, its a separate program that you'd have to download and install
on your machine(s). (Might have to compile from source for that matter).
The file that VMD produces is just a scene description file that
Rayshade can turn into an image. Its a ray tracer like Tachyon, POV-Ray,
etc, it just has the nice transparency feature for its images.

> I didn't see an option regarding "transparent" when using Rayshade
> though.

Its not an option within VMD, its a command line option you'd add
to tell it to render the image with a transparent background.
One of the people in our group used to use Rayshade a lot because she
liked the transparency feature, so this is why I'm familiar with its
use in this particular case.

> I'm trying to make a protein folding landscape in my ppt slide,
> and then put several protein configurations distibuted at the various
> location at the landscapes. However, because of the "frame" of the protein
> structure, my landscape looks kinda bad by overlaying with boxes.
> The goal is to use animation mode provided by the ppt and show these
> figures one at a time on the landscape, as if they are "rolling" down from
> the top of the landscape to the native state.

Well, I'd have to say that your picture will probably be worth more
than a thousand words, as I'm having a hard time imagining what you mean
with just this description. But, I think I get the general gist of what
you're saying. What's in your background besides the protein image?
Anything? Can you just set the background color in VMD to the same
color you're using in the slide? Are you using a gradient background in
the slide?

> Thank you, please help....
>
> I have photoshop element installed... but I havent used it before
> (pls forgive my ignorance in windows).

Hmm, well, I guess this is something you'd have to take some time to
figure out if you've never used it at all. I can't offer much photoshop
advice if you're completely at the beginning stages, as you won't know
what I'm talking about yet. If you play around with Photoshop or as
Brian Bennion suggested, GIMP, you can overlay images on top of each other,
make parts transparent, average them together, add them, subtract them,
all sorts of simple operations like these can be used to combine them.
This is normally how I'd recommend that you do things like make areas
transparent, since once you've learned, you can do it to any images you
like, not just ones that come from Rayshade with an alpha channel present.

Let us know if you need more help with this..
I'd bet someone has a tutorial for doing this sort of thing out on the
web already, if anyone knows of a URL, please feel free to post it...

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu
 

> On Wed, 5 Feb 2003, John Stone wrote:
>
> >
> > Hi Margaret,
> > If you render it with Rayshade, you can make a "transparent" background,
> > but this may be trickier than you're prepared to worry about just now, if
> > you've never used Rayshade before.
> >
> > Since you're using Powerpoint though, you should be able to place the
> > image behind all of the other items, so it shouldn't be necessary to
> > make it transparent. This can be done by using the object controls
> > to place it at the bottom of the stack. Unless you want other images
> > to "show through" or something, but that could be done with Photoshop
> > pretty easily, by compositing two images together. If you could tell us
> > more about what you're trying to do, it would be easier to help out.
> > You can also change the background color in VMD of course, by using the
> > Display->Background selection in the Color Form.
> >
> > Hope that helps,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Feb 05, 2003 at 05:06:41PM -0800, Margaret Cheung wrote:
> > > Dear All,
> > > I'm making some slides for the powerpoint presentation. I only need
> > > the image of the protein (without rectangle backgrounds) to make a flow
> > > chart. However, no matter how I do, the images are saved with backgrounds.
> > > Is there a way I can only take the image of the protein itself?
> > > Thank you.
> > >
> > > Sincerely,
> > > Margaret S. Cheung
> > > Physics Department 0319
> > > University of California, San Diego
> > > 9500 Gilman Drive,
> > > La Jolla, CA 92093-0319
> > > http://www-physics.ucsd.edu/~cheung
> >
> > --
> > 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
> > 

-- 
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