Hi Jérémie, I suspect the problems may be due to the large data size rather than using the hbonds command in per-frame scripting. It is common to combine hbonds with per-frame scripting of trajectories... it’s even in a tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part1> However, if you had a specific example of what you mean by not working, and the problem is reproducible (say on a smaller dataset that you could easily share with us), you could use menu: Help… Report a Bug. I’ll have to leave it to others with no-GUI scripting experience to say whether there is a way to get these results without displaying the trajectory frames. Sorry about the difficulties, 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 Apr 22, 2016, at 9:30 AM, Jérémie KNOOPS [531802] <Jeremie.KNOOPS@umons.ac.be> wrote:
Hi,
What is the easiest and fastest way to get the number of H bonds on every frame of a large trajectory (>10 000 frames) and print it to a file? The hbonds command does not seem to work with the perframe command and displaying the whole trajectory to run a per-frame script is quite slow.
Jérémie Knoops PhD Student