[phenixbb] Table 1 stastics

Nathaniel Echols nechols at lbl.gov
Thu Oct 18 08:19:01 PDT 2012

Sorry, I was not completely paying attention either.  One problem here
is that the scaling statistics are divided into 13 bins of uneven
size, whereas phenix.table_one always uses 10 bins, with equal numbers
of possible reflections in each bin (since this seems to be the most
common convention).  I should (and will) make the number of bins
adjustable, but clearly the statistics for the top bin in the XSCALE
log will not match what Phenix outputs, regardless of how they're
calculated.  This is another reason to move away from reliance on log
files and re-merge the data ourselves.

I'd still like to see the data file, however, as the completeness
calculated by Phenix is significantly lower and can't be accounted for
by the different binning.


On Thu, Oct 18, 2012 at 8:07 AM, Nathaniel Echols <nechols at lbl.gov> wrote:
> On Thu, Oct 18, 2012 at 7:53 AM, Andrew Waight <waight at msg.ucsf.edu> wrote:
>>       Thanks for Phenix! Anyway quick question, I tried out the "generate
>> Table1" utility for fun and noticed that my I/SigI and completeness do not
>> match what is found in my XSCALE file.
>> ...
>> How does Phenix compute these parameters? Obviously my I/sigI has gotten
>> much better (1.59 versus 0.85) but the scaling statistics should be the
>> correct ones.
> It computes these statistics directly from the reflection data you
> provide, not the log file.  (The reasoning being that since these are
> the data that Phenix actually uses, the statistics calculated from
> them are more accurate and relevant than whatever the scaling program
> thinks.)  My guess is that some of the internal processing accounts
> for the difference - could you please send me the data file?
> FYI, the plan for the future is to recalculate all of these statistics
> from unmerged data rather than rely on parsing data processing
> logfiles, which obey no standard format and are subject to change
> without notice.
> -Nat

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