A standard orientation is anything you want it to be and is usually
defined in the context of orthogonal axes. It is simply a reference
point from which you apply the results of your search. We usually
use one or more of the orthogonal axes as a starting point for easier
visualization.
To define a 3-fold axis for a locked search in GLRF (if I understood
your message correctly):
locsym 90.0 90.0 120.0 3 polar
This defines a standard orientation for that 3-fold. The search will
then move the 3-fold by the given parameters to new orientations and
calculate the peak height at those grid points after applying 3-fold
NCS. Which axis this actually defines as your standard orientation
and how it is then moved during the search depends on your choice of
conventions for orthogonalization and polar angle searches.
Cheers,
Jeff
On Apr 1, 2009, at 3:32 PM, Francis E Reyes wrote:
I am experimenting with GLRF and am having trouble calculating the
locked self rotation function for a protein of known structure.
The protein has a 3 fold NCS axis that is not parallel to a
crystallographic axis. I'm at the step of specifying the local
symmetry elements for the locked self rotation function.
I guess the goal here is to search for 'one general rotation which
will bring the non crystallographic symmetry point group in a
"standard" orientation. What does this mean? How do I write the
LOCSymmetry instruction for the input file?
My s.g. is P 21 21 21 and the following solutions are found for the
normal self rotation function.
Fine searches around peaks with the slow rotation function --
The large-term cut-off is 1.50
Listing of the fitted angles of the top 5 peaks --
No. Old Angles S A N G L
E O A N G L E Old Ht. New Ht.
(polar,
XYK) (polar, XZK)
phi psi
kap phi psi kap
1 52.000 50.000 120.000 52.000 50.500
120.000 53.246 127.449 120.000 417.36 420.74
2 128.000 130.000 120.000 128.000 129.500
120.000 233.246 127.449 120.000 417.36 420.74
3 128.000 50.000 120.000 129.000 50.000
120.000 126.870 126.536 120.000 400.32 407.69
4 52.000 130.000 120.000 51.000 130.000
120.000 306.870 126.536 120.000 400.32 407.68
5 44.000 60.000 120.000 42.000 61.000
120.000 36.719 125.820 120.000 385.56 391.96
The goal of all this is to use GLRF to explore NCS in cases where
structures are not known and molecular replacement
Thanks
FR
---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
