[Chimera-users] Measure correlation for rotated map positions

Tom Goddard goddard at sonic.net
Thu Jul 3 16:14:55 PDT 2014

Hi Rakesh,

  The “measure correlation” rotationAxis option only accepts a specification of two atoms to define the rotation axis.  This is explained in the Chimera documentation.


  Specifying 3 numbers is not enough since you need both a direction and a point on the axis.  If you have a center x,y,z position and axis vector ax,ay,az then you could use the “turn” command to do the rotations and the “measure correlation” command without the rotationAxis option as follows.

	perframe "turn 0,0,1 10 center 0,0,0 coord #1 model #1 ; measure corr #0 #1" frames 36

This does a rotation by 10 degrees about center 0,0,0 and axis 0,0,1 using map #1 coordinates then measures the correlation between map #1 and #0, repeating this 36 times (covering 360 degrees).  Results are reported in the reply log.



On Jul 3, 2014, at 2:56 PM, Rakesh Ramachandran  wrote:

> Hi,
>     I wanted to know how can I measure correlation starting from a fit and rotating the model around an axis with respect to the map. I tried calculating the centroid of the model and then rotate it using measure correlation but it did not work, the rotationAxis field was not taking the x,y,z position of the centroid of the model.
> Regards
> Rakesh

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