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If the structures are from not-perfectly-isomorphous crystals
or different ncs-related molecules in the same crystal,
you want to do this in two steps:
First find an operator that superposes one domain, and move a
copy of the structure to that position. Then find the operator
taking the second domain from its position in the structure
superimposed by the first operator, onto itself in the second
operator.

Or equivalently find the two operators, one superimposing
each domain, and divide (multiply one by inverse of the
other) to get the ratio.

There are programs that will analyze this kind of
conformational change and some even make pictures with
the rotation axis drawn in. Maybe ncsgroups, dyndom, theseus?


Hidong Kim wrote:
> 
> Hi, Ben,
> 
> Try lsqkab.  Do a superposition of the before and after coordinates of 
> the domain.  The log file will have the rotation matrix and the 
> translation vector.  Good luck,
> 
> 
>*Benjamin Brooks:
> Sent by: CCP4 bulletin board <[log in to unmask]> 
> I was wondering if anyone had a simple way of describing a conformational
> change by measuring the rotational and translational displacement of a
> domain from a starting structure.
> Thank you,
> Ben B
>