Hi Bala, (1) sidechain <-> mainchain H-bonds only. You cannot define two groups of atoms, group1 and group2, and then request only group1<->group2 H-bonds. However, you can define a group and request only the group<->non-group H-bonds. You would do that by selecting the atoms in the group, for example, command: select @n,ca,c,o which would select the mainchain, and then use "selRestrict cross" with the "findhbond" command, or if you are using the FindHBond GUI, choosing the option to "Only find H-bonds with exactly one end selected." Actually only the N and O would make H-bonds anyway, so you could just select @n,o instead. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findhbond.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond...
What might be the easiest is to make a copy of your structure, and in that copy delete everything that is not sidechain or mainchain. For example, command: delete ~ protein Then with the group selected and the options set as described above, you would only get mainchain<->sidechain H-bonds. (2) distance and angle cutoffs. There is no single distance or angle cutoff, there are different values for each combination of donor-acceptor atom types. The cutoff values were taken from a publication as described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond...
<http://www.ncbi.nlm.nih.gov/pubmed/9007693> The values in the publication were based on very high-resolution small molecule structures, so typically for PDB structures more lenient values are used, where the tolerance values are added to the cutoffs taken from the publication. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jul 22, 2009, at 2:52 AM, Bala subramanian wrote:
Friends,
I want to see the hydrogen bond between only side chains & only main chain. 1) I want to know if there is any easy way to do this in chimera
2) What is the default distance and angle used in chimera for calculating the hbond. I see that distance tolerance is 0.4 and angle tolerance is 20. Do these values mean default distance and angle.
Thanks, Bala