[Chimera-users] Time evolution of the crossing angle between helices during MD trajectories

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 27 10:58:21 PDT 2017


Hi George,
What you get from choosing two axes in  the "Axes/Planes/Centroids” table is not the distance between their center points, but their closest distance (along the whole axes).  You also get the crossing angle.  
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>

You would need to use MD Movie per-frame scripting, with commands: define axes with the “define” command and measure their crossing angle with the “angle” command.  That way you could get a value reported to the Reply Log at each frame.  After defining the script, you would need to clear the Reply Log, then go to trajectory frame 1 and  run through the whole thing once with looping turned off, then save the results from the Reply Log  to a text file for further processing, for example, keeping only the lines with “Angle".  (You might have done this before for distances or H-bonds.) 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>

You can’t use the MD Movie plotting for this purpose; it only does angle calculations for atoms.  The reason is that it is clear which atom is the same atom in different trajectory frames, but it is not clear which axis would be the same axis because you have to recalculate and replace them at each step, and they might be based on different sets of atoms at different steps as residues become more or less helical.

If your structure is constant enough that you think it will always have the same set of helices (even though they might change in length and position), then your “define” command could just recalculate all the helix axes in the structure, because then you could rely on the same IDs for the same two helices.  In other words if the structure will always have the same 8 helices, a per-frame script with something like the following would allow a valid comparison:

~define axes
define axis perHelix true
angle a4 a7

However, if there might be more or fewer helices at different frames in the trajectory, your “define” commands would instead need to reference specific residue ranges, which might not always be completely helical.

~define axes
define axis :10-18 at n,ca,c  number 1
define axis :58-66 at n,ca,c number 2
angle a1 a2

I tried something similar on an ensemble of 18 conformations, and then the lines with “Angle” from the Reply Log were:
Angle between a1 and a2 is 37.793
Angle between a1 and a2 is 20.357
Angle between a1 and a2 is 24.017
Angle between a1 and a2 is 7.086
Angle between a1 and a2 is 57.136
Angle between a1 and a2 is 25.112
Angle between a1 and a2 is 2.874
Angle between a1 and a2 is 22.765
Angle between a1 and a2 is 6.126
Angle between a1 and a2 is 23.888
Angle between a1 and a2 is 84.587
Angle between a1 and a2 is 5.281
Angle between a1 and a2 is 57.247
Angle between a1 and a2 is 50.152
Angle between a1 and a2 is 76.289
Angle between a1 and a2 is 16.187
Angle between a1 and a2 is 22.873
Angle between a1 and a2 is 28.225

You could choose to use different “define” options, like helical correction, etc. I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Sep 27, 2017, at 9:07 AM, George Tzotzos <gtzotzos at me.com> wrote:
> 
> In Chimera’s Structure Measurement tool, for a given protein, clicking on the Define axes gives the Cartesian coordinates of the centre of each helix as well as its direction. Selecting two helices (say helix 5 and 6) gives the angle and distance between these helices. I take it that the distance is defined as that between the centroids of the centre of mass of the two helices.
> 
> The question is whether it is possible to work out the time evolution of the crossing angle between to helices during an MD trajectory. 
> 
> MD Movie/Analysis/Plots/Angles plots the angle between three atoms rather than the crossing angle of the chosen helices. Am I right? Missing something?
> 
> Thanks in advance for your help
> 
> George




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