*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
Y. -F. Li wrote:
Hello,
Is there a program for calculating the center of gravity? For a
2-domain structure, what is the best and acurate way to measure the
angle between the two domains?
Hi Yong,
If you only have one structure, then defining an angle between domains
is a bit arbitrary. You need to define a hinge-point and the centres of
the two domains.
If you split your pdb file into files containing one domain each, a
number of programs, including moleman, pdb-mode can tell you the mean of
those coordinates (which is approximately the centre of mass of the domain).
If you have two structures of the identical molecule with different
hinge angles, then dyndom (ccp4) can give an explicit description of the
difference between them and help you locate a hinge point.
Alternatively, if you can compare with a related structure, you can fool
dyndom into working by doing some clever superimposing and editing of
one of the structures.
In principal, a molecular dynamics run on your single structure could
give you a set of structures to compare with dyndom, and thus define a
hinge point.
A different approach would be to use moleman2 (command XYz
ALign_inertia_axes) to calculate the vectors describing the major
principal intertia axis of your individual domains, and calculating the
angle between these vectors. This angle would not be pinned to any hinge
point and so might be meaningless depending what you want it for.
Cheers,
Charlie
--
Charlie Bond
Professorial Fellow
University of Western Australia
School of Biomedical, Biomolecular and Chemical Sciences
M310
35 Stirling Highway
Crawley WA 6009
Australia
[EMAIL PROTECTED]
+61 8 6488 4406
