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