Would this work?
Take the rot-trans operator from superpose or lsqman and express
the rotation matrix as polar coordinates of rotation axis (and angle about it).
Get the rotation axis as direction cosines, which will be a vector along
the rotation axis of the matrix. Now take the component of the
translation vector along that rotation axis, and subtract from the
translation vector, to get the component of the translation vector
which is orthogonal to rotation axis. Divide that by two and,
as a vector from the origin, it defines a point on the
rotation axis. Add any multiple of the rotation axis vector to
this and it gives another point on the rotation axis.
Test these points by operating on them with the orig
rot-trans operator, they should just move along the rotation axis
by the screw component of the rotation
WENHE ZHONG wrote:
Dear members,
I would like to have your ideas if there is any way to identify a rotation
centre of
domain in two different states using CCP4 or other program.
The situation is: the domain of the protein will rotate between two different
states
(depending on substrate binding) around 8 degree, and it is (nearly) clearly
that the
domain is rotated around a rotation centrel. So the question is how to identify
this
"rotation centre" in this 3D model? The ideal is to identify a region of
residues in the
domain which are most closed to the rotation centre.
The tool I am using right now is the "superpose" tool in CCP4 package. The
output which I
think mightbe uesful is:
CENTROID OF "WORKING" MOLECULE : 157.812 152.396 -70.778
CENTROID OF "WORKING" MOLECULE :(fractional) 157.812 152.396 -70.778
CENTROID OF "REFERENCE" MOLECULE: 157.251 151.877 -70.874
CENTROID OF "REFERENCE" MOLECULE:(fractional) 157.251 151.877 -70.874
Distance between CENTROIDS : 0.770
Direction cosines of vector between CENTROIDS: 0.729 0.674 0.124
I would say the “CENTROID" it mentioned above, such as (157.251 151.877
-70.874), is
possibly near to the "rotation centre". I would like to have your opinion
though. Thank you.
King regards,
Wenhe
