WOW. There are so many ways to do it. Thank you all for replying.
Nian Huang
Department of Biochemistry
Univ of Texas Southwestern Medical Center
On 5/10/07, Charlie Bond [EMAIL PROTECTED] wrote:
Just to complete the set, in pdb-mode for emacs, if you do
pdb-increment-centroid 0 0 0 (e.g. to
Dear Nian,
staying within CCP4:
% echo END | pdbset xyzin your.pdb
will print something like
Orthogonal Coordinate limits in output file:
Minimum MaximumCentre Range
On X : 103.67119.61111.64 15.94
On Y : 58.62 93.54
You can use Coot to find the centre of mass. In the scripting window just
type:
in scheme:
(centre-of-mass yourmoleculenumber)
or in python:
centre_of_mass(yourmoleculenumber)
Bernhard
BTW the American spelling of centre (center) should work too...
Dear all,
I was trying to do a NCS
LSQKAB also tells you the centres of mass of the molecules you are fitting
Look in the log file (Centroid == centre of mass)
CENTROID OF WORKING MOLECULE : -87.717 116.189 1.694
CENTROID OF WORKING MOLECULE :(fractional) -0.180 1.170 0.010
CENTROID OF REFERENCE
Just to complete the set, in pdb-mode for emacs, if you do
pdb-increment-centroid 0 0 0 (e.g. to move a molecule to the origin), it
reports the original centroid.
Cheers,
Charlie
--
Charlie Bond
Professorial Fellow
University of Western Australia
School of Biomedical, Biomolecular and
Dear all,
I was trying to do a NCS averaging of the map using Resolve. I had a
partial model, which generated a rotation and translation matrix by
program lsqkab. Resolve also requires a center of mass input. Do you
know any program can estimate it either by map or pdb file?
Thanks.
Nian Huang
