[Chimera-users] Filled in/triangulated nucleotide base ring planes

Greg Couch gregc at cgl.ucsf.edu
Mon Jun 28 13:56:06 PDT 2004

A preliminary version of what you want, without documentation, is 
available at http://www.cgl.ucsf.edu/home/gregc/NucleicAcids.zip.  The
resulting NucleicAcids directory should be place in CHIMERA/share, where
CHIMERA is the directory where chimera was installed.

If you are using ribbons as well, then then you might wish to use the
Ribbon Style Editor and exchange the width and height values for the
Nucleic setting to effectively rotate the ribbon by 90 degrees.  More
work needs to be done to improve the ribbons for RNA.  DNA looks pretty 

Please send me any feedback, criticisms, accolades, suggestions for 
improvement...  I hope to get back to improving the interface in the
near future, so suggestions would be especially welcome.

 	Greg Couch
 	UCSF Computer Graphics Lab
 	gregc at cgl.ucsf.edu

On Mon, 28 Jun 2004, Pattanayek, Sabuj wrote:

> Date: Mon, 28 Jun 2004 13:00:33 -0500
> From: "Pattanayek, Sabuj" <sabuj.pattanayek at vanderbilt.edu>
> To: chimera-users at cgl.ucsf.edu
> Subject: [Chimera-users] Filled in/triangulated nucleotide base ring planes
> Hi,
> I was wondering if I missed this feature in Chimera somewhere...a way to fill in
> nucleotide base rings/planes, this is what I mean:
> http://linegli.mc.vanderbilt.edu/~sabuj/1GQU_ribbons.png (using ribbons v3.2)
> http://linegli.mc.vanderbilt.edu/~sabuj/1GQU_vmd.png (using vmd 1.8.2)
> If you've ever used Ribbons you know it's a real pain to setup. I actually ended
> up using Chimera's selection methods to create separate pdb files for inputs
> into Ribbon's scripts, and it doesn't do multi-colored surfaces/transparency
> very well.
> VMD as you can see is filling in the ribose sugars (which I don't want) and is
> failing to fill in some of the bases. I tried recompiling it's code with some
> modifications but failed due to some header problems.
> Anyways I was wondering if this feature might be added, if it already isn't
> there, with the ability to choose colors for the base rings, or attribute
> certain colors to groups of bases, etc.
> Thanks,
> Sabuj
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