On Tue, Jul 15, 2014 at 8:26 AM, Kenneth A. Satyshur <satyshur@wisc.edu> wrote:
"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.

Not "all possible", "all observed".  I've never seen any of the statistics in depositions (or Table 1, etc.) interpreted to include reflections that weren't actually measured in the experiment.  But different programs are not at all consistent about what "unique" means either: phenix.refine counts F+ and F- separately, Refmac (and the Table 1 program in Phenix) counts F+ and F- as a single reflection.

'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.

Other way around - unique is a subset of total.  My assumption would be that this refers to the number of reflections observed in the experiment, not accounting for symmetry or multiplicity, but it really depends on context.  (In our Table 1, "Total" = "separately integrated", prior to merging.)

You might consider checking the formal mmCIF definition as well:

http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/reflns.html

although to be honest some of these are pretty vague too.  Certainly the deposition server should give clearer instructions.  However, in the (near) future the task of PDB deposition should become much simpler and the various programs (including Phenix) will automatically take care of these issues for you.  (phenix.refine already has the ability to output mmCIF files directly, which may save you some time.)

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?

Many would argue that the traditional cutoff (e.g. I/sigma>2) is too conservative and throws out useful information; and most modern crystallography software (e.g. Phenix or Refmac) should behave sensibly with very weak high-resolution data.  I'm not going to rehash all of the arguments here, but we think that CC1/2 is a much more useful statistic for this purpose.  We definitely don't recommend applying any type of filtering beyond a single global resolution cutoff - so no filtering individual reflections, elliptical truncation, permanent anisotropy correction, or other selective removal/doctoring of data.

-Nat