ALMN can plot the rotation function as a map - although I challenge
anyone to make much sense of it! More or less the same methodology as
MOLREP.
More useful - it lists all peaks generated by the symmetry operators in
Eulerian, and polar angles and gives the direct cosines of the rotation
axes - you can then check which is related to which by trigonometry.
Eleanor
To repeat:
Hmm - this is tricky.
1) Presumably the size of your cell and your molecule determine how many
molecules you expect in an asymmetric unit. THE asym. unit for I4(1)22
is half that of I4(1) if the cell dimensions are the same so it is
reasonable to have 2 mols in I41 which generate a tetramer using the
crystallographic 2-fold -x,-y,z and 1 mol in I4122 which generates a
tetramer using the 2 perpendicular crystallographic 2 folds of I4(1)22,
-x,-y,z and y,x,-z.
2) A rotation function is not a Patterson - it is a function of
intensities, and can be visualised as an integration of the product of
overlapping patterson function within a spherical volume, but it cannot
be simpler plotted as a map.
ALMN ( an old MR program) did output a "map" of these values along the
Eulerian angles alpha, beta, gamma, but it is not very useful for
visualisation.
3) peak heights for the rotation function are not very reliable - and
without having the values I cant comment. You often get shoulders of
existing symmetry related peaks. Did you search with the monomer alone?
The solution usually comes out of the translation search.
Eleanor
Rajan Pillai wrote:
Hi All,
I want to plot the rotation function that MOLREP uses. I cannot find any
output of rotation function in the logfile or in moIrep.doc. I want to
locate the peaks of the rotation function, that are shortlisted as
solutions, which would help me in understanding the following problem.
My protein is a tetramer with 222 point group symmetry. In I4(1) space group
Molrep gives two molecules in the asymmetric unit with top two RF peak
heights 10 sigma and 6 sigma. The final solution is obtained from these
two peaks after TF search. Moreover in case of another protein with the same
tetrameric assembly and quite the same unit cell parameters, but in space
group I4(1)22, Molrep gives 1 molecule in the asymmetric unit; however, in
this case the peaks from the RF are 14 and 12 sigmas and the solution is
obtained from the first peak after TF search. In the input file I did not
mention the number of monomers to be searched. It detects that based on
Matthews coefficient.
I am a bit confused as to why in space group I4(1) the RF values are so
different. I would have expected them to be closer in values as they are
dimer. And also, in case of I4(1)22, the RF values also should be closer.
I was wondering if plotting the RF can help in understanding the relation of
the peaks and their values based on their location. I believe MOLREP
calculates RF over the whole unit cell, instead of the asymmetric unit.
Thanks,
Rajan
