On Oct 2, 2007, at 3:42 PM, E. Merkley wrote:
I am using chimera to visualize an MD trajectory. I want to look at the fluctuations of hydrogen bonding patterns in a helix over the course of the trajectory. Is there a way to use Find HBonds on each frame and display the updated pseudobonds as I view the movie in Chimera?
Hi Eric, Yes, there is a way, and it is even shown in one of the tutorials. With the MD Movie tool, you can define a simple script to be run at each step during playback. Part 1 of the "Trajectory and Ensemble Analysis" tutorial has examples of using either Chimera commands or python to run findhbond at each frame: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ ensembles2.html#part1 (that's the tutorial at our web site, but you can also get to the copy you downloaded with Chimera from the Help menu) You can generalize what is done in the tutorial, for example by using different options to the findhbond command. Thanks for your feedback and suggestions, we appreciate them - 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