VMD-L Mailing List

From: B. Bennion (bbennion_at_u.washington.edu)
Date: Thu Feb 06 2003 - 13:23:01 CST

Hello Margaret and other who may be interested,

>>gimp test.gif

This will start gimp and load the image file automatically

With the mouse on the image righ-click
you want to click on the menu option "Select"
within that new menu near the bottom is "Select by color" click this,

then with the mouse select the background of your image
at this point another window will open and will contain an outline of the
image you are working on

in this same window a selection box exist with a little button labeled
"inverse" click on this

now you have selected everything not the color of the background --your
protein

right-click on your mouse again and select the "edit" menu
then select "copy"
then select "paste as new"

a new window will appear with your selected image in it. The background
will be a checkerboard

Save this as a tiff file. Other formats won't work such as jpg gif png
That should be it..
If you have questions just ask
Brian

On Thu, 6 Feb 2003, Margaret Cheung wrote:

> Date: Thu, 6 Feb 2003 09:12:19 -0800 (PST)
> From: Margaret Cheung <cheung_at_physics.ucsd.edu>
> To: John Stone <johns_at_ks.uiuc.edu>
> Cc: B. Bennion <bbennion_at_u.washington.edu>, vmd-l_at_ks.uiuc.edu
> Subject: Re: Pls help me to render files with only traces of proteins!
>
>
> Dear All,
> Thank you so much for being considerable. I'm definitely interested in
> such an information for my next presentation!
>
> 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
>
> On Thu, 6 Feb 2003, 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
> >
>
>

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