I have to agree with Clemens and Eleanor. After I had come to the wrong conclusion about NCS and the number of molecules in the asymmetric unit several times I gave up using the self-rotation function. Nevertheless, I have been shown examples (especially NCS with Cn symmetry and unsual n) where the self-rotation function was spectacular.
George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Mon, 22 Mar 2010, Eleanor Dodson wrote: > 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 > > > > > > > > > > > > > >
