Hi Francis,
On Thu, Mar 18, 2010 at 09:03:13AM -0600, Francis E Reyes wrote:
Hi all
I have a solved structure that crystallizes as a trimer
I guess you mean that you have 3 mol/asu? And not just "a trimer in
solution that then forms crystals", right?
to a reasonable R/Rfree, but I'm trying to rationalize the peaks in
my self rotation.
That has very often fooled me: selfrotation functions can be very
misleading - at least in my hands (even using different programs,
resoluton limits, E vs F etc etc). Often peaks that should be there
aren't and vice versa.
The space group is P212121, calculating my self
rotations from 50-3A, integration radius of 22 (the radius of my
molecule is about 44). I can see the three fold NCS from my
structure on the 120 slice
Which one is it: the one at (90,90) or the one at (45,45)?
Or both?
but I'm trying to rationalize apparent two folds in my kappa=180. A
picture of both slices is enclosed. The non crystallographic peaks
for kappa=180, P222 begin to appear at kappa=150 and are strongest
on the 180 slice.
If you had a D_3 multimer (3-fold with three 2-folds perpendicular to
it) I could interpret those as
(a) 3-fold at (90,90)
==> 2-fold at ( 90,0) [direction cosines = 1.00000 0.00000 0.00000]
2-fold at (210,0) [direction cosines = -0.50000 -0.00000 -0.86603]
2-fold at (330,0) [direction cosines = -0.50000 -0.00000 0.86603]
(b) 3-fold at (45,45)
==> 2-fold at ( 90,315) [direction cosines = 0.70711 -0.70711 0.00000]
2-fold at ( 45,180) [direction cosines = -0.70711 0.00000 0.70711]
2-fold at (135, 90) [direction cosines = 0.00000 0.70711 -0.70711]
All those 2-folds axes have a 120-degree angle between them (obviously).
I might have the exact angles wrong (there could be slight offsets
from thoise ideal values and the self-rotation plot just piles the
peaks exactly onto crystallographic symmetry operators because of the
multiplicity of those symmetry elements) ... or maybe even more? But
for both 3-fold axes in the kappa=120 section I can convince myself
that there are the corresponding 2-folds to make up a D_3 multimer.
Since you probably only have space for 3 mol/asu, I would guess case
(a) to be the correct 3-fold NCS with the 2-folds in (a) resulting
from the 21 parallel to your 3-fold and the peaks in (b) resulting
from the remaining symmetry.
Does that fit?
Cheers
Clemens
My molecule looks close to a bagel (44A wide and 28A tall). The
three fold NCS is down the axis of looking down on the bagel
hole. I'm trying to find the two fold. I imagine it could be slicing
the bagel in half (like to eat it for yourself) or slicing it
vertically (like to share amongst kids) but I'm not exactly sure
what's the best way to visualize this. Is there something easier
than correlation maps with getax (since I have the rotation
(polarrfn) and translation?). If you have an eye for spotting
symmetry, Ill send the pdb in confidence.
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
