VMD-L Mailing List

From: Margaret Cheung (cheung_at_physics.ucsd.edu)
Date: Wed Feb 05 2003 - 23:41:50 CST

Dear All,

Thank you very much!
Suddenly I felt like myself being a retard for everything... I tried but
didn't see anything to "reverse the selection" by gimp on linux. I should
have investigated more time to improve my art skill.. But since my chair
was set on fire to meet a deadline for tomorrow. I'll just live by my
"boxes" floating on the energy landscape and pretend the audience won't
see it....
Thanks..
Sincerely,
Margaret

>
> 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
>
>