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
>
>
>
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