Yup, there is that. It doesn't help make the decision, though, of how
much to include. And the other problem is it requires higher redundancy
than I usually have when living on the edge of completeness vs death.
(It's not multiplicity-weighted, is it?)
(It's other problem is that it is hidden in the currently least
user-friendly program in crystallography -- as powerful as the algorithm
undoubtedly is; I argue that by definition a user-unfriendly program
cannot be considered powerful. But I digress. And provoke... and don
my flame-shield.)
phx.
Kay Diederichs wrote:
Hi Frank,
maybe this is an opportunity to state that there is indeed a way to
assess radiation damage by looking at an R-factor plot, but that
R-factor is R_d [1], not R_pim.
The formula and some explanation is in the CCP4 wiki at
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/R-factors#measuring_radiation_damage
best,
Kay
[1] Diederichs, K. (2006) Some aspects of quantitative analysis and
correction of radiation damage. Acta Cryst D62, 96-101
Frank von Delft schrieb:
Hi Manfred
thanks a lot for your comments, since they raise some interesting
points.
R_pim should give the precision of the averaged measurement,
hence the name. It will decrease with increasing data redundancy,
obviously. The decrease will be proportional to the square root
of the redundancy if only statistical errors or counting errors
are present. If other things happen, such as for instance
radiation damage, then you are introducing systematic errors,
which will lead to either R_pim decreasing less than it should,
or R_pim even increasing.
This raises an important issue. As more and more images keep
being added to a data set, could one decide at some point,
when to add any further images?
This really is the point: in these days of fast data collection, I
assume that most people collect more frames than necessary for
completeness. At least, I always do. So the question is no longer
"is this data good enough" -- that you can test quickly enough with
downstream programs.
Rather, it is, "how many of the frames that I have should I include",
so that you don't have to run the same combination of downstream
programs for 20 combinations of frames.
Radiation damage is the key, innit. Sure, I can pat myself on the
shoulder by downweighting everything by 1/1-N -- so after 15
revolutions of tetragonal crystal that'll give a brilliant Rpim, but
the crystal will be a cinder and the data presumably crap.
But it's the intermediate zone (1-2x completeness) where I need help,
but I don't see how Rpim is discriminatory enough.
phx.
