[Chimera-users] MD animation of electrostatic map

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 2 09:31:39 PST 2019

Dear Bala,
It’s not really a trick, just a procedure.  In the MD Movie tool you would define a per-frame script, with commands to open the APBS map for current frame, scolor command to color surface by map values, close map.  Probably you would need to name the map files by frame number and then use the frame-number substitution in the per-frame script.

Before you bother to define a per-frame script, you would of course just enter commands into the command line to check them for correctness and to decide what command options you want.

MD Movie per-frame scripting (MD Movie menu: Per-Frame… Define script):
… that dialog includes the option for frame-number substitution

Relevant commands include:  open, scolor, close  (I believe if you just show surface once at the beginning that will be enough)

Example of per-frame scripting in this tutorial:

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

> On Jan 2, 2019, at 3:51 AM, Bala subramanian <bala.biophysics at gmail.com> wrote:
> Dear Chimera users,
> I have a series of structures (tens of snapshots from MD) for which i have calculated the electrostatic potential (with APBS). I would like to know if there is any way,for instance using MD-movie plugin, to map the elect. potential corresponding to each structure so that i can actually visualize the changes in surface potential. All structures have been already fitted to a reference structure, hence there wnt be any rotation or translation.
> Any idea or trick to achieve such mapping would be greatly appreciated.
> Thanks,
> Bala

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