Re: [ccp4bb] R pim and Rmeans

[Kay Diederichs]

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





Frank von Delft schrieb:

[1] Diederichs, K. (2006) Some aspects of quantitative analysis and correction of radiation damage. Acta Cryst D62, 96-101

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?

phx.

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.

--
Kay Diederichs                http://strucbio.biologie.uni-konstanz.de
email: [EMAIL PROTECTED]    Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

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