correction:
Peak (21.44, 0, 180) has symmetry-related peak (158.56 180 180).
.....
On 23 Apr 2008, at 13:39, Derek Logan wrote:
Hi everyone,
Can anyone help me with interpretation of a self rotation function
and native Patterson from a dataset with pseudosymmetry? I've
always been a bit poor on spherical polars. The space group is P21
with beta = 92.2°. The kappa=180° section of the SRF, calculated
using Molrep, is at
http://mole.mbfys.lu.se/~derek/selfRF_180.png
and contains two big peaks around 7 sigma. I'm having trouble
identifying these in the list of peaks from Molrep:
theta phi chi alpha beta gamma
Isym_i Isym_j
Sol_RF 1 0.00 0.00 0.00 0.00 0.00 0.00 1 1
Sol_RF 1 90.00 -90.00 180.00 0.00 180.00 0.00 1 2
Sol_RF 1 90.00 90.00 180.00 0.00 180.00 0.00 2 1
Sol_RF 1 0.00 0.00 0.00 0.00 0.00 0.00 2 2
Sol_RF 2 158.56 180.00 180.00 0.00 42.89 -180.00 1 1
Sol_RF 2 111.44 0.00 180.00 -180.00 137.11 0.00 1 2
Sol_RF 2 111.44 0.00 180.00 180.00 137.11 0.00 2 1
Sol_RF 2 21.44 0.00 180.00 180.00 -42.89 0.00 2 2
Sol_RF 3 165.65 0.00 180.00 -180.00 28.70 0.00 1 1
Sol_RF 3 104.35 -180.00 180.00 0.00 151.30 180.00 1 2
Sol_RF 3 104.35 180.00 180.00 0.00 151.30 -180.00 2 1
Sol_RF 3 14.35 -180.00 180.00 0.00 -28.70 180.00 2 2
It seems to me to be two copies of peak 2. I believe theta starts
in the middle, perpendicular to the page and phi starts on the x
axis, thus the peak just below the centre would be (21.44, 0, 180).
I presume that the second peak is the symmetry-related (158.56,
180, 0)? However where is (111.44 0 180)? I would expect to see
this near the bottom of the plot, but it's not there. I'm sure I'm
missing something fundamental about the symmetry of the SRF
projection, but unfortunately I don't have a supervisor to bug
about this (I *am* the supervisor...)
In the native Patterson
http://mole.mbfys.lu.se/~derek/nativePatterson.png
there are two peaks of almost equal height. How can this be
reconciled with having only one strong peak in the SRF? There are
most likely two dimers in the asymmetric unit, but there may only
be one, with very high resulting solvent content. What's more the
molecules are leucine-rich repeat proteins and have weak internal
symmetry. I believe this was an issue with the ribonuclease
inhibitor, but looking briefly at the crystallisation article and
structure article I wasn't able to find a rationalisation of this
problem. The 2-fold is perpendicular to b*. How could this cause
the two peaks?
Thanks
Derek
