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
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 good. 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@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@vanderbilt.edu> To: chimera-users@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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Greg Couch -
Pattanayek, Sabuj