Thanks, I agree that CPPTRAJ is a great solution for analyzing trajectories. Looks like it can read several formats: https://amberhub.chpc.utah.edu/cpptraj/trajectory-file-commands/

Alternatively: In Chimera, if you can view your trajectory in the MD Movie tool, you can also use that tool to calculate and display an occupancy map. I think that's essentially the same thing that Tom mentioned, a density map on a grid that can be viewed as isosurfaces.

MD Movie help, click "Occupancy Analysis" in the left hand links: https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html

Occupancy analysis is also covered in the last section of this Chimera tutorial: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part2

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

On Feb 24, 2021, at 1:06 PM, Thomas Cheatham tec3@utah.edu wrote:

The program CPPTRAJ can bin ion densities on a grid which can be visualized with chimera...

See: https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-si...

CPPTRAJ is available in AmberTools or via GitHub - https://github.com/Amber-MD/

Also AmberHub may have a tutorial related - https://amberhub.chpc.utah.edu/making-a-3d-histogram/

--tec3

---

From: Chimera-users chimera-users-bounces@cgl.ucsf.edu on behalf of K Jan 10dunajkr@gmail.com Sent: Wednesday, February 24, 2021 1:53:36 PM To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] (no subject)

Hello,

I`ve just finished a simulation on DNA with K+ ions and I would like to get images of the average ion location at different points in the simulation.

I was wondering how I could find the average location of K+ ions ( because right now they`re scattered around the DNA) at different points of the simulation.?

Thanks