[Chimera-users] RNA ladder display

[Elaine Meng]

Hi Bala,
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.

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/nucleotides/nucleotides.html 
 >

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
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html



On Dec 15, 2009, at 8:25 AM, Bala subramanian wrote:

> Friends,
> 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.
> Cheers,
> Bala