[phenixbb] Table 1 stastics
Kay.Diederichs at uni-konstanz.de
Fri Oct 19 08:07:58 PDT 2012
I just want to point out that one possible source of discrepancy between
I/sigma reported by a data processing program, and I/sigma reported by a
program that uses the relevant cctbx routine is the following: that
cctbx routine calculates the variance of merged data as max("internal
variance", "external variance") which is different from what the data
processing programs do (they calculate the "internal variance" - I hope
I didn't get it the wrong way round). SHELXC and SHELXL also calculate
the variance of the merged data like the data processing programs do.
I dislike this "feature" of cctbx but I do not know if phenix.table_one
actually uses this routine for this purpose.
P.S. you can find the discussion over at the cctbx mailing list; see
and other posts.
On 10/18/2012 09:08 PM, phenixbb-request at phenix-online.org wrote:
> Date: Thu, 18 Oct 2012 08:07:44 -0700
> From: Nathaniel Echols<nechols at lbl.gov>
> To: PHENIX user mailing list<phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] Table 1 stastics
> <CALeAa1NDDy7=ZCUqThgun+k-Si7-Gf920ROvuYwpPgsShAhHVQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 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.
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: Kay.Diederichs at uni-konstanz.de Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
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