[Chimera-users] (no subject)

Tom Goddard goddard at sonic.net
Wed Apr 5 08:19:51 PDT 2017


The calculation of the symmetry axis was completely described in previous answers to your question.  The match maker command (mm) rotates a copy of dimer AB so that aligns with another copy BA by minimizing the RMSD between corresponding atom positions (an eigenvalue problem) and the the measure rotation command computes the rotation axis of that rotation matrix (a simple calculation on the matrix elements).  This is descrivbed in the command documentation as mentioned in previous replies to your question.  Please read the documentation.

   Tom

> On Apr 5, 2017, at 7:49 AM, Kavya Shankar <kavshank at umail.iu.edu> wrote:
> 
> Hi,
> 
> I would like to know how the axis of symmetry is calculated in a dimer as in the precise algorithm that is used to do this. 
> 
> Thank you.
> 
> Regards,
> Kavya Shankar
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