On 1/13/11 2:48 PM, J. Fleming wrote:
Hi All,
I'm about ready to deposit my structure and have used pdb_extract to
aid in the process. Unfortunately the following values were not found
and are required by ADIT:
1) Under Data Collection, Reflections section: Observed criterion
sigma(F) and Observed criterion sigma(I)
There is no criterion for sigma F applied in Denzo/HKL2000. Not least
of all because data processing programs like Denzo and Scalepack work
with intensities and not structure factor moduli.
The default Sigma(I) cutoff is -3
See:
http://www.hkl-xray.com/hkl_web1/hkl/Scalepack_Keywords.html (keyword
SIGMA CUTOFF)
2) Under Refinement, Refinement Statistics section: Number unique
reflections (all)
If your refinement program does not write it into the header of the PDB
file, and the description of the value does not make immediate sense to
you, omit it. Some of the requested values are defined rather vaguely.
A field matching this name doesn't show up in the REMARK 3 refinement
template for PHENIX-derived PDB files. (http://www.wwpdb.org/docs.html)
I haven't deposited lately but if I were to hazard a *guess* it might
approximate to the number of reflections you would have used in
refinement if you hadn't applied magnitude or sigma(F) cutoffs and prior
to PHENIX rejecting reflections as gross statistical outliers. One
straightforward way to get this number would be to use CAD to write a
new MTZ file containing only reflections within the resolution limits
used in refinement, and look in the log file to see what the output
reflection count was. Assuming, of course, that the cell dimensions
defined in your MTZ file are the same ones that you used in refinement.
Refinement programs vary in their policy about handling reflections
with |F|=0. The loss of reflections would manifest in a difference
between the completeness in data collection and the completeness in
refinement.
Phil Jeffrey
Princeton
