Hi Sze Yi
The simple answer is that if the indexing solution is correct, you
can't, and you shouldn't worry about this.
If you are worried, can you send me directly (i.e. *not* to the
ccp4bb!) the large date-stamped log file that will be called
something like "mosflm_20140820_145228.lp" so that I can have a look
at it to see if there's anything obviously wrong with your processing?
Provided that the values of refined parameters vary smoothly through
the processing run, you shouldn't be too concerned - 0.220mm is quite
large, but I see values like this pretty frequently - it's better to
consider the normal "Table 1" figures after scaling and merging.
Fixing the mosaic spread to a lower value will mean that you are only
using parts of the reflections near the middle of their rocking curve
to calculate the values (and also not measuring the tails in the
third dimension when integrating).
The mosaicity estimate is exactly that - it's better than a guess,
and in Mosflm is based on analysing the way that the overall
intensity measured changes with different values of calculated mosaic
spread (in iMosflm, this is done for the first image used in
autoindexing).
The important thing as far as Mosflm is concerned is that the
estimated value should be a good _starting_ value for refining it
properly, and is better than just having the value set to zero or
some other number that's been plucked out of thin air.
Unless you have a crystal with cubic symmetry, there is no reason why
the mosaicity should be isotropic (i.e. the same in all directions in
the crystal - after all, the cell dimensions will not be the
same...), so if you see the value change for different orientations
of the crystal, that's what (in general) you should expect.
On 23 Sep 2014, at Tue23 Sep 09:38, Lau Sze Yi wrote:
Hi,
I collected a dataset using our home source (Rigaku/MSC FR-E
SuperBright; -AXIS IV++ imaging plate detector) and am processing
my data using imosflm.
Autoindexing solution is P222, with an estimated mosaicity of 1.20.
Mosaicity tends to refine to as high as 1.6, RMS residual ~ 0.220.
If I fix the mosaicity at lower values , RMS residual drops. Does
this mean that the mosaicity was overestimated in the first place?
How do I make sure that mosaicity is not over or under estimated.
Appreciate your feedback.
Regards,
Sze Yi
Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick
Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9
(Crystallographic Computing)
