[Chimera-users] ribbons of nucleic acids

Conrad Huang conrad at cgl.ucsf.edu
Wed Sep 1 14:48:44 PDT 2004

Ann Mullin wrote:
> Hello,
> I am wondering how to adjust the ribbons of nucleic acids so that they 
> follow the path of the phosphates or the sugars, anything but the 
> averaged path they have now.  I want to show the backbone as a ribbon 
> with bases projecting out, but now some bases float about the backbone.
> Thanks for any help.  Ann

I just modified Chimera to accept user-defined "ribbon residue classes", 
which specify the ribbon-guiding atoms (currently we use C5' for nucleic 
acids).  Unfortunately, the changes had to be made at the C++ level, 
which means you would need a complete new distribution.  We plan to have 
a new snapshot release in a few weeks, but if you'd like to try it out 
sooner, we can try to arrange something.  (You'll need the new Chimera 
and a script for creating "ribbon residue classes" for now, but we may 
have an extension for manipulating these classes in the future.)


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