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Axel Brunger had an X-PLOR script to do exactly this sort of thing with
the Fab fragment of the antibody 26-10 that was one of his molecular
replacement test cases. Rummaging around I see it's called "elbow.inp"
so if you have a working X-PLOR installation you might find it in:
xplor_3.851/tutorial/xtalmr/elbow.inp
but all this does is do a specific rotation about an axis running
through two atoms - you can derive direction cosines for the axis based
on two atoms, and I'd hope that some program allows you to specify them.
If all else fails, and assuming you've got two points that define the
elbow/rotation axis:
* move coordinates such that point #1 as at (0,0,0)
* rotate coordinates around origin such that point #2 lies on the Z axis
* construct rotation matrix using the formula:
cos(kappa) sin(kappa) 0.0
-sin(kappa) cos(kappa) 0.0
0.0 0.0 1.0
where kappa is the desired rotation angle, and this is just the polar
angle rotation matrix equation with phi=psi=0.0
* apply rotation matrix to relevant part of molecule
Although, perhaps if the MR solution finds both halves of the receptor
with good statistics, it0's telling you something, even if it's not
where you expect it to be ?
Phil Jeffrey
Princeton
Patrick G. Shaw wrote:
I was wondering if anyone knows of a way to perform molecular replacement
about a specific hinge region, I have heard rumors of a program that exists for
this very reason but have not been able to find it.
