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

[George Tzotzos]

Hi Elaine,

Sorry to bother you again on the same subject.

As I mentioned earlier, your script worked just fine. At this point, and for one frame only, I’d like to generate an image showing the distance between the two centroids. I tried to do it by the pseudo bond command to no avail. I’m sure there’s a way to do this but I haven’t been able to work it out. 

Any help would be most welcome.

Regards

George

> On 27 May 2016, at 19:02, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 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
> 
> <1plx-image.png>
> 
> On May 27, 2016, at 1:30 AM, George Tzotzos <gtzotzos at me.com <mailto: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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