I'd say you'd probably want to dump a list of the H bonds to a file in both programs (easy in Chimera at least) and find the differences and then look at the structure where the differences occur and assess for yourself which program is doing a more accurate assessment of the hydrogen bonding. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jan 28, 2010, at 2:53 PM, Elaine Meng wrote:
Different programs use different methods and cutoffs. You could try setting the tolerances to 0.0 if you feel the default Chimera method is too permissive, but there is no reason to expect exactly the same number of H-bonds from two different programs. You would need to look at VMD documentation to see how theirs are calculated, and at Chimera's (link already sent in previous message) to know how they are calculated, then decide which one you want.
In Chimera, the angle and distance cutoffs depend on the atom types, and the criteria depend on published data (the small molecule structures). In many other programs, the same cutoffs are used no matter which atom types are involved. I don't know how it is done in VMD, however.
I know of one paper where the authors tried both MolProbity (a fancier method) and Chimera and said they usually gave the identical H-bonds: Differences in the risk of celiac disease associated with HLA-DQ2.5 or HLA-DQ2.2 are related to sustained gluten antigen presentation. Fallang LE, Bergseng E, Hotta K, Berg-Larsen A, Kim CY, Sollid LM. Nat Immunol. 2009 Oct;10(10):1096-101
Elaine
On Jan 28, 2010, at 2:36 PM, snoze pa wrote:
Hi Elaine, Thanks for your help. But somehow I am getting different number of bonds in vmd and chimera. A snap shot of the figure is shown below.
http://img191.imageshack.us/img191/9084/screenshotva.png
In VMD the Hbonds are calculated by show Hbonds and protein. Vms shows 24 hbonds while chimera shows 38 hbonds. I don't know how to justify this. I will highly appreciate your help. A snapshot is shown in the link http://img191.imageshack.us/img191/9084/screenshotva.png
Thanks s
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