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/nucleot...
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@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