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

Terwilliger, Thomas C terwilliger at lanl.gov
Fri May 31 18:15:27 PDT 2013

```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.

So in xtriage:

TWINNED STRUCTURE:

Wilson ratio and moments

Acentric reflections
<I^2>/<I>^2    :1.667   (untwinned: 2.000; perfect twin 1.500)
<F>^2/<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>/<I>^2    :1.995   (untwinned: 2.000; perfect twin 1.500)
<F>^2/<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>/<I>^2    :2.939   (untwinned: 3.000; perfect twin 2.000)
<F>^2/<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: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Michael Thompson [miket at chem.ucla.edu]
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 <L^2>=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<cctbx::miller::index<int>, scitbx::af::trivial_accessor> miller_indices, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> 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<cctbx::miller::index<int>, scitbx::af::trivial_accessor> miller_indices, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> 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" <nechols at lbl.gov>
To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
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 <Samuel.Stampfer at tufts.edu> 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
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--
Michael C. Thompson

Biochemistry & Molecular Biology Division

Department of Chemistry & Biochemistry

University of California, Los Angeles

miket at chem.ucla.edu
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