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
