[Chimera-users] Hidden capability to compute all bonds on a per-frame basis

[Elaine Meng]

Hi Benjamin,
You can catalog H-bonds over every frame in a trajectory one frame at a time (there is no need to have all the H-bonds for all frames exist simultaneously). Using the MD Movie tool, just add a per-frame script that runs the “findhbond" command, similar to what’s done in Part 1 of this tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html>

You would include the save-to-file option in that “findhbond” command (if you wanted a separate output for each frame), or use the logging option and then save the Reply Log to file afterwards.  This is a common use of Chimera.

If you really did need the H-bonds for all frames to exist simultaneously (a reason might be for faster interactive playback of the trajectory with H-bonds), I note that ChimeraX has this capability:

See ChimeraX “hbonds” command (“coordsets” option)
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html>

ChimeraX doesn’t have many tool graphical interfaces yet, but lots of functionality in commands: “open” to open trajectories, “coordset” to play them back (and there is also a relatively simple slider graphical interface):
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html>
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html>

The input trajectory formats are more limited, multi-model PDB or mmCIF plus those listed here:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 19, 2018, at 11:48 AM, benjamin.horsman at alumni.ubc.ca wrote:
> 
> Hello,
> A 2014 message to chimera-users mentioned that "There is also a hidden capability in Chimera to compute all bonds on a per-frame basis."  (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-April/009759.html)
> 
> Could someone please elaborate on this?  Does this functionality still exist is recent versions of Chimera, and has it been documented anywhere?
> 
> My requirements are just that - to catalogue all (hydrogen) bonds over every frame in a trajectory.
> Thank you,
> BGSH