[Chimera-users] RNA ladder display
meng at cgl.ucsf.edu
Tue Dec 15 08:42:51 PST 2009
Currently you cannot control how many hydrogen bonds are required for
ladder display -- it will show a bar where there at least one hydrogen
bond between the two residues. You can only control whether hydrogen
bonds to any part of the residues are counted, or only those between
base atoms (i.e. not the sugars or the phosphates). This setting is
in the "ladder options" in Nucleotides.
The ladder options also allow you to use previously calculated H-bonds
or adjust the H-bond criteria, and in that way you may be able to get
just the ladder bars you want. The cutoff number of H-bonds would
still be 1 rather than 2, however.
I hope this helps,
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Dec 15, 2009, at 8:25 AM, Bala subramanian wrote:
> I have a RNA structure. I want to calculate hydrogen bonds between
> the bases (for which i used findhbond menu). Then i want to show the
> ladder representation for those base-pairs which form atleast two
> hydrogen bonds. How can i do the same. Hope i am clear.
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