[Q] Molecular Graphics?

Phil Jeffrey phil at xtreme1.mskcc.org
Wed May 24 16:32:26 EST 1995

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

>>   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.

>> 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).

If you are using Molscript and Raster3D (molscript -r option) on an SGI, you
can acheive something that *looks* like this, as follows:

render an image with the blocking residues in place
render an image *without* the blocking residues in place
use the "blend" command to merge these two files together

This is *not* formal transparency of the second image, and lighting will
complicate the image slightly, but may be close enough to do what you want.
(This method requires that you are using RGB format images on an SGI).

Just an idea (looks OK when I test it)
Phil Jeffrey

| Phil Jeffrey                                  |                             |
| X-ray/Computer Manager, Crystallography Lab   | If you lie to the compiler, |
| Memorial Sloan-Kettering Cancer Center, NYC   | it will get its revenge     |
| phil at xray2.mskcc.org, p-jeffrey at ski.mskcc.org |     - Henry Spencer         |
| Ph: (212) 639 2189   Fax: (212) 717 3066      |                             |

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