[Chimera-users] Detection of Internal water along MD trajectory

Elaine Meng meng at cgl.ucsf.edu
Thu Mar 20 10:58:26 PDT 2014

Hi James,
After setting up the basic display (i.e. show ribbon, hide atoms/bonds), use the command line to work out the commands that you want to run at each trajectory frame.  For example, if your residue of interest is 57 in chain A, maybe something like:

~disp solvent
disp solvent & :57.a z<5

Then once you have decided on which commands you want, just use per-frame scripting in the MD Movie dialog, e.g. choose from MD Movie menu: Per-Frame… Define script and enter those commands as a Chimera command script to be run at each movie frame.

This is documented here

… and there are further examples in the "Trajectory and Ensemble Analysis" tutorial:

You might also want to take a look at that tutorial to get more familiarity with MD Movie in general. The second part has an example of the occupancy calculations that Eric mentioned. 

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 20, 2014, at 3:15 AM, James Starlight <jmsstarlight at gmail.com> wrote:

> Hi Elaine,  Eric,
> many thanks for suggestions!
> This time I'd like just visualize water influx into the protein interior seen during molecular dynamics trajectory. 
> Previously I did such analysis in VMD but due to some problems with understanding of Chimera's selection lets consider my example more closely here. 
> E.g I've defined some geometrical center (specifying some residue which is situated within of my protein interior) and than would like to (1) select all water within 5 A of this residue and (2)  using MD movie plugin make such selection in each trajectory frame and visualize it along with the cartoon representation of my protein only (hiding all another solvent). I'll be thankful if you provide me with some example of such task.
> James

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