[Chimera-users] Measuring angles and distances between planes defined by two aromatic rings

Elaine Meng meng at cgl.ucsf.edu
Fri May 27 10:02:56 PDT 2016


Hi George,
You can define centroids and measure the distance between them, and define planes and measure the angle between them.  You can do this for specific snapshots, or in MD Movie you can define a per-frame script and have it execute at every frame and report results to the Reply Log.

In my example data (PDB 1plx, NMR ensemble opened as trajectory from MD Movie), I tried this per-frame script (MD Movie menu: Per-Frame… Define script), Chimera commands:

echo frame: <FRAME>
define centroid number 1 radius 0.5 :1 at cg,cd1,cd2,ce1,ce2,cz
define plane number 1 :1 at cg,cd1,cd2,ce1,ce2,cz
define centroid number 2 radius 0.5 :4 at cg,cd1,cd2,ce1,ce2,cz
define plane number 2 :4 at cg,cd1,cd2,ce1,ce2,cz
distance c1 c2
angle p1 p2

… which gave output like this in the Reply Log:

[…]
frame: 09
centroid name, ID, center: centroid: c1 ( -2.594,   2.758,  -1.103)
plane name, ID, center, normal, radius: plane: p1 ( -2.594,   2.758,  -1.103) ( 0.798, -0.576, -0.180) 1.399
centroid name, ID, center: centroid: c2 (  2.361,  -0.549,   1.599)
plane name, ID, center, normal, radius: plane: p2 (  2.361,  -0.549,   1.599) (-0.725,  0.288, -0.626) 1.395
Distance from c1 to c2 is 6.541
Angle between p1 and p2 is 50.860
frame: 10
centroid name, ID, center: centroid: c1 ( -2.613,   3.441,  -0.814)
plane name, ID, center, normal, radius: plane: p1 ( -2.613,   3.441,  -0.814) (-0.650,  0.693,  0.310) 1.399
centroid name, ID, center: centroid: c2 (  1.560,  -0.777,   1.955)
plane name, ID, center, normal, radius: plane: p2 (  1.560,  -0.777,   1.955) (-0.749,  0.092, -0.657) 1.394
Distance from c1 to c2 is 6.548
Angle between p1 and p2 is 69.698
[…]

You would give different residue numbers and atom names to define the centroids and planes in your own data, but otherwise it would be basically similar.

I also attached an image of my example system with the centroids and planes shown.

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


On May 27, 2016, at 1:30 AM, George Tzotzos <gtzotzos at me.com> wrote:

> Having generated a 100ns trajectory, I’m interested in measuring the time evolution of the distance between to aromatic ring centroids as well as the angle between the planes of these two rings. The idea is to determine if I’m dealing with pi-pi stacking interactions.
> 
> I’ve check past correspondence and tried various permutations of commands to no avail. Maybe my best option is to do this for selected snapshots and define for each snapshot two centroids (e.g. c1 and c2) and measure the distance c1 c2. I haven’t managed to find a solution for measuring the angles between the two planes defined by the ring atoms.
> 
> I’d appreciate any suggestions on possible solutions to the problem described above. I’m attaching a snapshot of measuring distances between two atoms (not really a good solution).
> 
> Thanks in advance
> 
> George
> 
> <PastedGraphic-2.pdf>
> 
> 
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