I absolutely agree with Clemens; self rotation functions can mislead in
some cases, and confuse in many more.. A peak in a self rotation does
NOT mean you have a dimer or a trimer - just that one molecule in the
asu can be related to another by the given operator. So for any peak
ther are nsym*2 possible positions..
However old fashioned programs like polarrfn, almn, and amore list all
symmetry equivalents of each peak which often illuminate things, and you
often notice that the expected 3-fold generates 2 folds when combined
with symmetry operators.
You dont give the angles of your 3 fold, but if phi=45, omega = 36, the
combination with crystallography 2 folds generates non-crystallographic
two-folds in the a-b plane..
Eleanor
Clemens Vonrhein wrote:
> 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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