[Chimera-users] Generating trajectory of a user-defined plane

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 18 16:08:43 PDT 2013

Hi Lili,
Yes, you can do it with a per-frame script in MD Movie.

First figure out the "define" command including its options and specified atoms that defines the plane you want.

Then in MD Movie menu, choose "Per-Frame... Define script" and enter the same command except assigning a different ID than the first plane, plus the command "angle" to measure the angle between the planes with those two IDs.   For example, if I had plane p1 defined by all alpha-carbons, I would then enter as the Chimera command script:

define plane number 2 @ca
angle p1 p2

Then click OK, then show (in Chimera menu under Favorites) and clear the Reply Log, then play the trajectory from start to end without looping.  At each trajectory frame, it will recalculate plane p2 and the p1-p2 angle. The angle values will be in the Reply Log.


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 Apr 18, 2013, at 3:46 PM, Lili Peng wrote:

> Hi,
> I am interested in measuring the deviation of an helical segment with respect to the initial structure in a GROMACS trajectory.  I have already uploaded my *.tpr and *.trr files into MD Movie and have defined a plane through the helical segment within the initial structure.  Is it possible to define another plane through the same helix and track the intersection angle throughout the trajectory?
> Thank you,
> Lili

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