Hi Tassos,
I tried to summarize the discussion (or rather, some parts of it) in
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Test_set
Anybody is welcome to improve on this!
Kay
Anastassis Perrakis schrieb:
> Hi-
>
> I am afraid that the real issue might be that the real question is:
>
> 'How do I tell the referee of my paper that 1500 reflections are enough?'
>
> Something along the lines of a statement like:
>
> "It is generally accepted by the X-ray crystallography community that
> 1000-1500 are far enough for estimating Rfree, and in fact as few as
> 150 reflections can be enough. for a reference the editor could check
> the ccp4bb archive or the crystallography wikis and references therein"
>
> Now ... thats fun ...:
>
> The IUcr Wiki says:
>
> "A fixed percentage of the total number of reflections is usually
> assigned to the free group."
>
> And it references only the MiE paper of Axel in 1997 where I read:
>
> In all test calculations to date, the free R value has
> been highly correlated with the phase accuracy of the atomic model. In
> practice, about 5-10% of the observed diffraction data (chosen at random
> from the unique reflections) become sequestered in the test set. The size
> of the test set is a compromise between the desire to minimize statistical
> fluctuations of the free R value and the need to avoid a deleterious effect
> on the atomic model by omission of too much experimental data.
>
> I could not find the full text of the 1992 paper.
>
>
> CCP4 [User Community] Wiki
>
> The 'user' one has links to the IUcr Wiki and the "test set" article is
> still not written.
> The 'official' one does not touch the subject either.
>
> Time to write it (with appropriate references!!!) ?
>
> Tassos
>
>
>
> On Jun 16, 2008, at 20:21, Mark J. van Raaij wrote:
>
>> Dear All,
>>
>> It has recently been put to me that 5-10% of reflections should always
>> be set aside for calculation of Rfree. However, when one has, say, 200
>> 000 reflections (high resolution and/or large asymmetric unit), that
>> seems to me to be a waste, because it would mean removing 10 000 to 20
>> 000 reflections from the refinement target.
>>
>> My opinion is based on discussions with a particular knowledgeable
>> crystallographer and a meeting report (
>> http://journals.iucr.org/d/issues/1996/01/00/li0216/li0216.pdf ), in
>> which 1000 reflections is said to be enough (i.e. statistically
>> valid). As a result, I always take 1000-1500 reflections,
>> independently of the number of total reflections, adjusting the
>> percentage or the width of the thin shells (in case of NCS) accordingly.
>>
>> What is the opinion of the community? And, if you agree with me, how
>> should we try to get this opinion (more) generally accepted?
>>
>> On a related note, how to refine a structure with only 5000
>> reflections, which could happen when you have a small a.u. and modest
>> resolution? Could, exceptionally, a lower absolute amount of
>> reflections be used for Rfree, say 500?
>>
>> Greetings,
>>
>> Mark
>>
>>
>> Mark J. van Raaij
>> Dpto de Bioquímica, Facultad de Farmacia
>> Universidad de Santiago
>> 15782 Santiago de Compostela
>> Spain
>> http://web.usc.es/~vanraaij/
>
--
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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