VMD-L Mailing List

From: B. Bennion (bbennion_at_u.washington.edu)
Date: Wed Feb 05 2003 - 21:13:34 CST

Hello Margaret,

If I remember correctly you do have a linux box somewhere right? GIMP can
be installed and used much more effectively than the adobe products.. (my
humble opinion)

I would change the background color in VMD to white and save/render the
image. The image can be opened with gimp. Once in gimp you can select by
color, white in this case. An option will appear to reverse the selection
and this can be used to grab the protein from the background. It can then
be saved in another image file for use in ppt.

Brian

 On Wed, 5 Feb 2003, Margaret Cheung wrote:

> Date: Wed, 5 Feb 2003 17:48:33 -0800 (PST)
> From: Margaret Cheung <cheung_at_physics.ucsd.edu>
> To: John Stone <johns_at_ks.uiuc.edu>
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: Pls help me to render files with only traces of proteins!
>
>
> 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).
> I didn't see an option regarding "transparent" when using Rayshade
> though.
>
> 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.
>
> Thank you, please help....
>
> I have photoshop element installed... but I havent used it before
> (pls forgive my ignorance in windows).
>
> 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
> >
>
>

Graduate Research Assistant
Dep. Medicinal Chemistry, University of Washington
Tel# (206)616-2779
BOX 357610 Seattle WA 98195

email--bbennion_at_u.washington.edu
web page--http://students.washington.edu/bbennion