Perhaps this video would be helpful:
http://www.cgl.ucsf.edu/chimera/videodoc/AlignDomains/index.html
The "axis point" shown in the reply log at the very end is what I
think you want.
BTW, the video is a little out of date, in that if you get the very
latest daily build the MatchMaker tool can match the smaller domains
with having to delete part of the structure.
--Eric
On Nov 23, 2011, at 4:00 PM, 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.
