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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