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/
