And, in the case of translational non-crystallographic symmetry or tNCS (where the particular special case of pseudo-centering is most serious), Phaser can now correct for the statistical effects. This works pretty well when there's only a single tNCS translation, but the corrections aren't (yet) as robust when there's more than one tNCS translation. Best wishes, Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 1 Jun 2013, at 02:15, "Terwilliger, Thomas C" 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. 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.

So in xtriage:

TWINNED STRUCTURE:

Wilson ratio and moments

Acentric reflections /<I>^2 :1.667 (untwinned: 2.000; perfect twin 1.500) <F>^2/ :0.857 (untwinned: 0.785; perfect twin 0.885) <|E^2 - 1|> :0.609 (untwinned: 0.736; perfect twin 0.541)

NOT TWINNED STRUCTURE:

Wilson ratio and moments

Acentric reflections /<I>^2 :1.995 (untwinned: 2.000; perfect twin 1.500) <F>^2/ :0.788 (untwinned: 0.785; perfect twin 0.885) <|E^2 - 1|> :0.732 (untwinned: 0.736; perfect twin 0.541)

Centric reflections /<I>^2 :2.939 (untwinned: 3.000; perfect twin 2.000) <F>^2/ :0.648 (untwinned: 0.637; perfect twin 0.785) <|E^2 - 1|> :0.990 (untwinned: 0.968; perfect twin 0.736)

If this test says your crystal is not twinned, it probably is not twinned.

All the best Tom T

________________________________________ From: [email protected] [[email protected]] on behalf of Michael Thompson [[email protected]] Sent: Friday, May 31, 2013 3:50 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Discrepancy between R-factors from phenix.refine vs phenix Generate "Table 1"

As another follow up to this point, I have had a recent example where Xtriage reported that my intensity statistics indicated twinning (<|L|>=0.399 and =0.227, alpha=0.4). After having refined the structure with the suggested twin law, and making composite omit maps along the way (using autobuild with no twin law), I ran model vs. data at the end of refinement and noticed that it reported R/Rfree that were about 10% higher than the R/Rfree from refinement, similar to what the original post described. I checked the model vs. data logfile and found that the L-test routine used by model vs. data was failing, so the subsequent analysis was carried out as if there was no twinning.

So in my case, the crystal was twinned, but model vs. data was not able to perform the L-test so it was outputting incorrect R-factors.

The error message at the top of the model vs. data log file is:

Twin analysis failed: Python argument types in l_test.__init__(l_test, miller_index, double, space_group, bool, float, float, float, int) did not match C++ signature: __init__(_object*, scitbx::af::const_ref miller_indices, scitbx::af::const_ref intensity, cctbx::sgtbx::space_group space_group, bool anomalous_flag, long parity_h, long parity_k, long parity_l, unsigned long max_delta_h) Twin analysis failed: Python argument types in l_test.__init__(l_test, miller_index, double, space_group, bool, float, float, float, int) did not match C++ signature: __init__(_object*, scitbx::af::const_ref miller_indices, scitbx::af::const_ref intensity, cctbx::sgtbx::space_group space_group, bool anomalous_flag, long parity_h, long parity_k, long parity_l, unsigned long max_delta_h)

Perhaps there are some other users who are seeing this behavior because the L-test fails within model vs. data.

Mike

----- Original Message ----- From: "Nathaniel Echols" To: "PHENIX user mailing list" Sent: Wednesday, May 29, 2013 5:18:57 PM GMT -08:00 US/Canada Pacific Subject: Re: [phenixbb] Discrepancy between R-factors from phenix.refine vs phenix Generate "Table 1"

On Wed, May 29, 2013 at 4:13 PM, Sam Stampfer wrote:

...

When I refined my model in phenix, I used the twin law h,-h-k,-l. I read in the documentation that twinning can account for some of this discrepancy, but that the program is supposed to take twinning into account if it will lower the calculated R-work by more than 2%, which it doesn't seem to have done (or there is some other problem with my data).

Okay, the problem is that your data don't actually appear to be twinned. The automatic method used by phenix.model_vs_data (which is used internally for Table 1 and the validation GUI) only tries possible twin laws if the results of the "L test" show a suspicious distribution of intensities. Your data look fine, so it doesn't bother trying the twin laws. That the R-factors are lower when you refine with a twin law isn't necessarily indicative of the data actually being twinned - Garib Murshudov has looked into this in detail but I confess to being ignorant of the math (but I can probably dig up his paper on the subject if anyone is interested). However, I'm pretty sure the data are actually in a higher-symmetry space group. Will send details and new files off-list (probably tomorrow at this rate).

I should probably change some of the programs and/or documentation to make it more clear what is being done internally, since it took me a bit of digging to realize what was going on. In general, though, always be very careful before running twinned refinement! I have seen several users do this by mistake when they really had higher symmetry. The maps will also be more model-biased when using twinned refinement, so it's good to avoid doing this unless absolutely necessary.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Michael C. Thompson

Graduate Student

Biochemistry & Molecular Biology Division

Department of Chemistry & Biochemistry

University of California, Los Angeles

[email protected] _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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: [email protected] [[email protected]] on behalf of Edward A. Berry [[email protected]] 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" 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. 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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