I think that 'observed' goes back to whether it was possible to see a
reflection (and estimate its intensity by eye) on the photographic FILM.
In small molecule crystallography it is usually understood to mean
F4sigma(F) (or I2sigma(I)).
George
On 07/15/2014 07:02 PM, Edward A. Berry wrote:
So on second thought, practically speaking I guess observed is all,
since we never see the ones that are rejected by the -3 sigma
observed criterion
On 07/15/2014 12:44 PM, Edward A. Berry wrote:
I don't think observed means all the reflections that were integrated,
becasue one of the other parameters is the criterion for a reflection
to be considered observed, so that observed is a subset of all.
Here are some lines I saved from an adit2 session (some years back,
but I believe it was the same in a recent deposition)
I don't think the questions fit very well the way we collect and
process data today, but I think most of these are optional.
What I called Rsym should probably be called Rmerge,
from merging frames not merging crystals.
Observed criterion sigma(F) null
Observed criterion sigma(I) -3
Resolution (high) 3.000
Resolution (low) 42.68
Number unique reflections (all) ?
Number unique reflections (observed) 141782
Percent possible (observed) 91.8
R-merge I (observed) ?
R-sym I (observed) 0.124
On 07/15/2014 11:26 AM, Kenneth A. Satyshur wrote:
There is some disagreement on terms used to deposit data. We need a
definition and an algorithm
for each definition.
Unique Reflections
My definition is all the possible reflections out to the highest
resolution reported not related by symmetry.
Where can I find this? The .mtz contains a list of all HKL
calculated to the highest resolution. Usually, we
are not able to measure all these diffraction spots due to limits of
the detector, mechanical limits, crystal
orientation, etc.
'Total reflections'
The depositions server asks for total reflections. I assume it wants
only those unique reflections we were able to
collect, regardless of the sigma cut off. These are called
'observed'. The total we use in refinement will be a subset
of the 'unique observed' that are cut on sigma. However, some
crystallographers believe that we should not cut
on sigma since some of the intensities may in fact be zero. Is this
a question for the Refmac and Phenix people?
Please give us some guidance and maybe a reference or two that we
can use.
thanks
--
Kenneth A. Satyshur, M.S.,Ph.D.
Senior Scientist
University of Wisconsin
Madison, Wisconsin 53706
608-215-5207
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Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582
