Hi Jacob, If you have a sufficient number of unique reflections, use percentage because it is more convenient. If not, at least make sure the below criteria are met. If that's not possible, don't use maximum likelihood for refinement ;-)
Cheers, Tim On 11/21/2014 05:09 PM, Keller, Jacob wrote: > Agree with all of this—but how does it reflect on the original question of > whether to use a percent or an absolute number? > > JPK > > From: Pavel Afonine [mailto:[email protected]] > Sent: Friday, November 21, 2014 11:02 AM > To: Keller, Jacob > Cc: [email protected] > Subject: Re: [ccp4bb] Free Reflections as Percent and not a Number > > Hello, > > choice of the size of free (or test, whatever you like to call them) > reflections is important for three different purposes: > > - estimation of parameters for ML target for refinement; > - map calculation (coefficients m&D in 2mFo-DFc or mFo-DFc map are calculated > using test reflections); > - validation (calculation Rfree). > > It is important that free reflections are evenly distributed across the whole > resolution range, and each sufficiently thin resolution bin contains at least > 50 test reflections so that the estimation of ML parameters is robust and > reliable. "Sufficiently thin resolution bin" is such that ML parameters can > be assumed constants in it. > > Smaller test sets will result in less stable refinements (refinement outcome > will strongly depend on the choice of test set). > > Larger test sets will damage map quality (unless all reflections are used in > map calculation). > > Size of free set needs to be sufficiently large so that Rfree is > statistically meaningful. > > Nothing new is said above, it's all documented in the literature! > > Pavel > > > On Thu, Nov 20, 2014 at 2:43 PM, Keller, Jacob > <[email protected]<mailto:[email protected]>> wrote: > Dear Crystallographers, > > I thought that for reliable values for Rfree, one needs only to satisfy > counting statistics, and therefore using at most a couple thousand > reflections should always be sufficient. Almost always, however, some > seemingly-arbitrary percentage of reflections is used, say 5%. Is there any > rationale for using a percentage rather than some absolute number like 1000? > > All the best, > > Jacob > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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