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 On Thu, Jan 28, 2010 at 3:16 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi S, If you are recording a movie file, just do it for every step. The playback will be slower but the resulting movie will not. If you are just doing it for your own viewing, it is up to your own judgement how often it should be done. Most accurate would be every step that is in your trajectory, but that will slow down the playback.
As described in the manual, <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html#criteria> findhbond uses several different distance and angle cutoffs depending on the donor and acceptor atom types. Those cutoffs are based on very high-resolution small molecule structures, and we have found that for PDB structures in general (macromolecules and typically not as high resolution) the results are best with some relaxation of the strict values. So for example if the strict cutoff is 1.0 A, with 0.4 tolerance, the resulting cutoff would be 1.4 A. Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 28, 2010, at 1:06 PM, snoze pa wrote:
Thanks Elaine for your prompt reply. Do you think if it is good to calculate the hbonds after every 10ps snapshot from hbonds menu. I want to count how many hbond are lost with time. When I am using this trick then I can see no more broken hbonds. Also another question related to Relax constraints, it is 0.4 A; what that mean? is it same as donor acceptor atom distance? thank you. S