Hi Chimera crew, 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? Also, may I take this occasion to point out that requiring consecutive frames to have consecutive numbers in the file names is inconvenient. For instance, my simulation is 41 ns long, and the structures are stored (in our in-house format) every 1 ps. So rather then write out 41000 .pdb files, I'll write them out every 10 or 100 ps. To use chimera to view a movie, I have to rename the files using a perl script. Incidentally, I've been using Chimera for 3 years now and love it. -Eric Merkley Graduate student Biochemistry Department University of Washington
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
Hi Eric, I have some things to supplement Elaine's answer. There is a feature in Chimera's Python layer for speeding up H-bond analysis of trajectories that is currently only available to scripts. The feature is caching the identification of the donors/acceptors of a structure so that it doesn't have to be redone for each frame. I've now added code so that it is available in the hbond command as the "cacheDA" keyword (value should be true or false). Empirically, turning caching on speeds up the trajectory playback by more than a factor of two. One way to get the feature is by downloading a test build newer than October 1 from http://www.cgl.ucsf.edu/chimera/alpha- downloads.html . However, I'm aware of some other problems in those builds so I don't necessarily recommend that right now (the problems _should_ be fixed in a week or so though). What you can do instead is edit Chimera's Python code to add the keyword yourself. You would need to edit the file: <your Chimera installation>/share/FindHBond/base.py (on a Mac you need to control-click on Chimera.app and choose "Show Package Contents", then in the new Finder window maneuver to Contents/ Resources/share/FindHBond) You need to add the keyword to the createHBonds function and subsequent calls to findHBonds. If you are using the 1.2422 release, change line 852 from: reveal=False, namingStyle=None, log=False, to: reveal=False, namingStyle=None, log=False, cacheDA=False, line 902 from: interSubModels=interSubmodels) to: interSubModels=interSubmodels, cacheDA=cacheDA) and line 930 from: interSubModels=interSubmodels) to: interSubModels=interSubmodels, cacheDA=cacheDA) With these changes, you can use the command "hb cache true" in the MD Movie scripting interface to show H-bonds using caching.
Also, may I take this occasion to point out that requiring consecutive frames to have consecutive numbers in the file names is inconvenient. For instance, my simulation is 41 ns long, and the structures are stored (in our in-house format) every 1 ps. So rather then write out 41000 .pdb files, I'll write them out every 10 or 100 ps. To use chimera to view a movie, I have to rename the files using a perl script.
The non-consecutive thing hadn't even occurred to me, so thanks for pointing it out. I'm responsible for a lot of parts of Chimera so don't nearly as much time to work on MD Movie as I would like, so it may be some time before I am able to do anything to remedy this. I'll open a change-request in our bugs database with you cc'ed so you'll know when something happens --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
participants (3)
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E. Merkley -
Elaine Meng -
Eric Pettersen