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we have NCS rotation (158.56, 180, 0) - rotation matrix [R] and we have two CS operators (P21) - rotation matrix (0 0 0) [1] and (90 90 180) [2]. So, all symmetry related (for [R]) rotations are [1][R][1] = [R] - (158.56, 180, 0) [1][R][2] = [R][2] - ( 111.44 0.0 180.0) [2][R][1] = [2][R] - ( 111.44 0.0 180.0) [2][R][2] - (21.44, 0, 180) Really we have two rotations, because (158.56, 180, 0) and (21.44, 0, 180) are idendical. There is nothing special. If there is pure dimer one rotation is pure 2-fold axis another is 2-fold axis with translation. Alexei On 23 Apr 2008, at 22:29, Derek Logan wrote: > Thanks to everyone who helped with the self RF problem: Eleanor, > Ian, Claudine, Pietro & Alexei. > > Eleanor wrote: > >> 1) It is a bit hard to find out how MOLREP defines its orthogonal >> axes - many programs use X0 || a, Yo || b* and in P21 hence Zortho >> is || to c* >> If that is what Molrep does then your 2 fold is in the a c* plane, >> 21 degrees or 111 degrees from c*. >> The 2 peaks you see are symmetry equivalents. > > This was my interpretation. Glad we agree ;-) The documentation > says "A parallel to X , Cstar parallel to Z" > >> As for the Patterson - what height are those peaks relative to >> the origin? > > The peaks are u = 0.129, v = 0.473, w = 0.220 (20% of origin peak > height) and u = 0.180, v = 0.500, w = 0.248 (19%). What I don't get > is why there are two and only one strong 2-fold. 2 dimers in the AU > gives 50% solvent, 1 dimer 75%. The crystals diffract to 2.3Å, > which would tip the balance in favour of 50% solvent in my opinion. > >> With 2 dimers in the asymm unit and with the non-cryst 2-fold >> perpendicular to b* you could have such translations between one >> monomer and another. > > Would the 2-folds of both dimers have to be very similarly > oriented? Maybe one peak masks the other at this resolution? > >> is there a model - easiest to solve it then analyse this sort of >> stuff later! > > Believe me, we've been trying for a very long time! The problem is > that it's a leucine rich repeat protein with under 30% sequence > identity to any of the other LRR models out there. I think the > failure of MR is down to a combination of a) the low homology, b) > the pseudosymmetry, c) the nature of the LRR, which means you can > get MR solutions that are out by one or more repeats. Maybe even > the internal symmetry of the whole LRR structure can add to this > pathology? We've had some solutions that looked almost right, but > we can never see much more than what's already in the MR solution. > > Ian wrote: > >> The symmetry of the self-RF is explained in detail in the >> documentation for POLARRFN, in fact I would advise you to use this >> because you can then plot monoclinic space groups with the unique >> b axis along the orthogonal Z axis (NCODE = 3) and then the >> symmetry is *much* easier to interpret. > > The reason I started using Molrep was that POLARRFN always used to > choke on these data. However that problem seems to have > disappeared. Using ORTH 3 indeed gives a more interpretable plot, > as you say. > >> According to polarrfn.doc the symmetry generated by a 2-fold along >> b parallel to Z is (180-theta, 180-phi, kappa) so the peak in the >> list (159,180,180) is the same as (21,0,180) which is a NCS 2-fold >> that you can see just below centre. The peak (111,0,180) is thus >> the same as (69,180,180) near the top which is another NCS 2-fold >> perp to the first generated by the crystallographic 2-fold. > > Indeed, I see the peak (69, 180, 180) but I don't find it in the > list in the log file from Molrep. I thought that list was supposed > to be exhaustive. Also the plot is not well documented for Molrep. > I wrote to the BB a while ago to ask what the contour levels were > but no-one answered. By Googling I found a crystallisation paper > where it was described as "from 0.5 sigma in steps of 0.5 sigma" > but that information appears to have come by word of mouth. Also, > is it just the "north hemisphere", as Claudine put it, that is > plotted? > > Anyway, I feel somewhat wiser now... > > Derek >