[Chimera-users] angle between subunits

[Elaine Meng]

Hi Jiri,
If you are going to use Axes/Planes/Centroids it would make more sense to define a plane for each monomer (not axes) and then measure the angle between the planes.  The main difficulty is that you only want to use the homologous and structurally similar parts to calculate the planes, which might require listing specific residue numbers.  However, if you feel that the folds of the two subunits are similar enough that you could use all residues, it could be something like commands:

define plane :.a at ca
define plane :.b at ca

…and then in the Axes/Planes/Centroids dialog, just choose both planes (highlight both rows) with the mouse and it will report the angle between them (or use a command, e.g. “angle p1 p2” depending on what the planes are named).  You might have to add/subtract 180 from the result depending on your intuition.

However, it will always be slightly different depending on what atoms you use to define the planes.  I wouldn’t say it is “biased” but instead that you should try to only use the backbone or CAs of the parts that you think are structurally very similar between the two subunits.

The result from “match" (or “measure rotation”) is the angle around their axis of symmetry, which is a different thing and probably not what you wanted.

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 Nov 26, 2016, at 8:47 AM, chemocev marker <jirivitali at gmail.com> wrote:

> Hi All
> 
> I am interested to measure the angle between chain A and chain B of heterodimer, and both sequence identity is around 14%. I can measure the angle by selecting 3 atoms on chain A and chain B but this is bias because, if I change the residues then the angle will be different.
> 
> I can also measure by structure measurement options and defining the axes and all the create axes for all the helices in the chain A and chain B and measure the angle between two helices on chain A and chain B. I am not sure if its a right way to claim the angle between chain A and chain B in one PDB file. 
> 
> I also try to use the 
> "match :.A at CA :.B at CA move false show true"
> 
> But it gives the rotation angle. As I am comparing the different homologous structureswhere chain B shows more identity but the each structure have a different state giving a unique angle between chains.
> 
> What can be best option to measure this???
> best
> 
> Jiri
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