VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 06 2003 - 13:55:43 CST

Hi,
  Mauricio had a couple of suggestions for useful GIMP info which I've
forwarded below, also take a look at Brian Bennion's latest email,
he's got nice instructions for making transparent images with gimp.

----- Forwarded message from Mauricio Carrillo Tripp <tripp_at_fis.unam.mx> -----

Date: Thu, 06 Feb 2003 13:56:55 +0000
From: Mauricio Carrillo Tripp <tripp_at_fis.unam.mx>
To: John Stone <johns_at_ks.uiuc.edu>
Subject: Re: Pls help me to render files with only traces of proteins!

You can check these out

www.gimp.org
gimp-savvy.com/BOOK/

John Stone wrote:

> Hi,
> Good suggestions. Brian, do you know of a GIMP tutorial she
> can follow for this sort of thing? Its easy to use if you've
> ever used Photoshop etc, but to a complete newbie I bet its still
> a bit intimidating... If anyone has tutorial URL's, they'd probably
> be very helpful for Margaret and others wanting to make nice slides..
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Feb 05, 2003 at 07:13:34PM -0800, B. Bennion wrote:
> > 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
>
> --
> 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

----- End forwarded message ----- 

-- 
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