[Q] Molecular Graphics?

Bob Litt r-litt at uchicago.edu
Wed May 24 02:35:00 EST 1995

In article <3ptdrl$3s6 at decaxp.harvard.edu>, Timothy Jackson
<tjackson at fas.harvard.edu> wrote:

> I am trying to design a cover submission for Science for a submitted 
> report on the spectroscopy of myoglobin. I wish to show the entire 
> protein and the ligand as rendered spheres and the heme as sticks.  This 
> part is no problem. However, I want to make the atoms that block the heme 
> pocket from the viewers perspective translucent so that the heme pocket 
> and the ligand are visible to the viewer.  Does anyone have any good 
> ideas (I have tried Quanta and Molscript to no avail).

I do not know if this would satisfy your needs, but if I were trying to do
this I would probably use RasMol.  I have been using the Macintosh
version, and I understand it is also available for PC and a few other
platforms.  You could render most of the hemoglobin as space filled
representations, represent the heme as sticks, and then specifically
select the atoms that you want to render as "dot" surfaces to create a
sort of "translucent" effect.  If the dots are not adequate to your
"translucence" needs, then I am afraid you will need to export the program
into Adobe Photoshop or something similar to acheive the special effects
you want.

Bob Litt

r-litt at uchicago.edu
Segev Lab
Department of Molecular Genetics and Cell Biology
University of Chicago

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