[phenixbb] Discrepancy between R-factors from phenix.refine vs phenix Generate "Table 1"

Terwilliger, Thomas C terwilliger at lanl.gov
Sat Jun 1 12:43:16 PDT 2013

The L test should be insensitive to the space group the data are processed in. Sorry I caused that confusion.

Yes, the Wilson ratio test is an intensity moments test.  Note that correction for anisotropy, if present, is essential, and as Randy pointed out, phaser can also correct for the effects of pseudo-centering.

-Tom T

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Edward A. Berry [BerryE at upstate.edu]
Sent: Saturday, June 01, 2013 9:34 AM
To: PHENIX user mailing list
Subject: Re: [phenixbb] Discrepancy between R-factors from phenix.refine vs phenix Generate "Table 1"

Comparing below, i'm confused about the ability of the "L" test to distinguish twinning from underestimated symmetry.
And is the Wilson Ratio test an intensity moments test?

On 1 Jun 2013, at 02:15, "Terwilliger, Thomas C" <terwilliger at lanl.gov> wrote:

> I think it is important to remember that perhaps the best statistic we have right now for identification of whether a structure is twinned is the Wilson ratio  <I**2> / <I>**2. For acentric reflections this is 2.0 for untwinned and 1.5 for perfect twin.   This can of course be complicated by pseudo-centering.  Aside from that issue, it is a really good indicator.
> It can be better than using the L test or others that compare reflections because it does not require that you have the correct symmetry.

On 7 September 2012 09:10:19 GMT+01:00 Randy Read wrote:
>> Twinning tests that compare the intensities of potentially twin-related reflections to see if they are more closely related than expected randomly (e.g. the H test or the Britton plot) can't tell the difference between twinning and either higher symmetry or pseudosymmetry.  So you need to use a test based on intensity distributions independent of twin laws (like the intensity moments or the L test) to decide if your crystal is twinned, then if it is twinned you will get a better idea of the twin fraction from tests comparing the twin-related reflections.

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