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