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I've tried jmol but I would like the carbons to stand out as clearly as it does in this model and thus it would be great if I could use black for carbon, white for hydrogen, blue for nitrogen and red for oxygen. I am running 32 bit 12.10.

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I prefer VMD (link). You'll have to complete some license information in order to download, but its graphical user interface is easy to use and you have the most control over all the atoms and their properties.

You'll need to load the coordinates of the molecule and then change the representation.

(If you don't want to go through the entire download/install process, consider Rasmol - link)

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How do I register for a VMD login? –  Brenton Horne Apr 18 '13 at 15:28
    
Your 32 bit download is here: ks.uiuc.edu/Development/Download/… Just enter a NEW username and passwd. –  philshem Apr 18 '13 at 17:54
    
Rofl, sorry I didn't read that part. OK and how do I install this? –  Brenton Horne Apr 18 '13 at 18:09
    
thismagpie.blogspot.com/2012/11/… but not the 64 bit version –  philshem Apr 18 '13 at 18:40
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