[ccp4bb] More on truncate ignorance

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Unexplained electron density
From: Maria_Håkansson maria {- dot -} hakansson {- at -} MAXLAB {- dot -} LU {- dot -} SE
Date: 2008-09-19

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From: "William G {- dot -} Scott" wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-09-19

Subject: More on truncate ignorance
From: "Dunten, Pete W {- dot -} " pete {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2008-09-19

I hadn't realized phenix.refine handles this differently.

If I start with an mtz file from truncate, with F, SIGF, IMEAN, SIGIMEAN all available,
the default for phenix.refine seems to be to work with IMEAN, SIGIMEAN.

From the log file . . .

Intensities converted to amplitudes for use in refinement.

Number of F-obs in resolution range: 266875
Number of F-obs <= 0: 22532
Refinement resolution range: d_max = 25.4557
d_min = 2.0000

Fobs statistics after all cutoffs applied:

Miller array info: None
Observation type: xray.amplitude
Type of data: double, size=244343

And then later in the log . . .

============================== Outliers rejection =============================

basic_wilson_outliers = 186
extreme_wilson_outliers = 128
beamstop_shadow_outliers = 9
total = 197

And this gives 244146 reflections to use in refinement.

So it looks as if the weak data simply disappears.

Pete

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Unexplained electron density
From: Maria_Håkansson maria {- dot -} hakansson {- at -} MAXLAB {- dot -} LU {- dot -} SE
Date: 2008-09-19

Next message:
Subject: Re: Facebook for Neerds
From: "William G {- dot -} Scott" wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-09-19