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 On Thu, Jan 28, 2010 at 1:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi S, The H-bonds do not automatically recalculate. Instead of using findhbond one time before playing the trajectory, it should be used at each step. This can be done with a per-frame script. On the MD Movie player dialog, choose "Per-Frame... Define script" and specify that the script is in "Chimera commands." Then enter whatever commands you want to execute at each step. The MD Movie documentation includes an example with calculating H-bonds: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>
In your case it could be as simple as one "findhbond" command. First, I recommend trying the command in the regular Command Line to figure out which keywords and options you want. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html>
If there are protein ribbons shown, another command you might want to include in your per-frame script is "ksdssp" to recalculate secondary structure assignments. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>
The Trajectories tutorial, part 1, also includes using a per-frame script to calculate H-bonds: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part1>
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
On Jan 28, 2010, at 10:51 AM, snoze pa wrote:
Dear Chimera Users, I am analyzing a MD trajectory in chimera. After selecting H binds when I am playing the trajectory, then it always shows the hydrogen bond. Though some of the bonds are broken during the simulation but it always connect the step 1 h bonds connected.. How can I show the h bonds which breaks during the simulation. Thank you very much for your help. S