Interesting. I checked my data in P4 with xtriage and yet L-test comes at a respectable 0.948. How does one assess pseudo rotational symmetry in the refined structure? Thanks FR On Apr 27, 2009, at 8:48 AM, Peter Zwart wrote:

...

I have yet to find a twinning test that can assess perfect twinning.

I think you mean perfect twinning in the presence of pseudo rotational symmetry. Without the latter part, The L-test works very well.

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--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

R vs R statistic: R_abs_twin = <|I1-I2|>/<|I1+I2|> Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95 R_abs_twin observed data : 0.012 R_abs_twin calculated data : 0.300 Is R_abs_twin the same thing as Robs_twin in Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95 ? And I guess I have rotational pseudo symmetry with Rcalctwin < 1/2. Interestingly when I run xtriage when the data is scaled into P 41 21 2 I get the following stats R vs R statistic: R_abs_twin = <|I1-I2|>/<|I1+I2|> Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95 R_abs_twin observed data : 0.012 R_abs_twin calculated data : 0.521 since r_abs_twin or r_obs_twin ~= 0, that's an indicator for perfect twinning. FR On Apr 27, 2009, at 8:58 AM, Peter Zwart wrote:

Try supplying a pdb file

phenix.xtriage mydata.sca reference.structure.file=mymodel.pdb

for the RvsR analyses.

P

2009/4/27 Francis E Reyes :

...

Interesting. I checked my data in P4 with xtriage and yet L-test comes at a respectable 0.948. How does one assess pseudo rotational symmetry in the refined structure?

Thanks

FR

On Apr 27, 2009, at 8:48 AM, Peter Zwart wrote:

...

...

I have yet to find a twinning test that can assess perfect twinning.

I think you mean perfect twinning in the presence of pseudo rotational symmetry. Without the latter part, The L-test works very well.

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--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder

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8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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-- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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On Apr 27, 2009, at 9:20 AM, Peter Zwart wrote:

...

R_abs_twin observed data : 0.012 R_abs_twin calculated data : 0.300

Is R_abs_twin the same thing as Robs_twin in Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95 ?

And I guess I have rotational pseudo symmetry with Rcalctwin < 1/2.

Correct.

...

Interestingly when I run xtriage when the data is scaled into P 41 21 2 I get the following stats R vs R statistic: R_abs_twin = <|I1-I2|>/<|I1+I2|> Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95

R_abs_twin observed data : 0.012 R_abs_twin calculated data : 0.521

since r_abs_twin or r_obs_twin ~= 0, that's an indicator for perfect twinning.

when data is scaled in P 41 21 2 and you still get twin laws, it means your cell still has higher symmetry. what are your unit cell parameters?

Sorry Peter I err'd. When the data is scaled in P 41 21 2, xtriage reports the summary twinning analysis as follows: ------------------------------------------------------------------------------- Twinning and intensity statistics summary (acentric data): Statistics independent of twin laws - /<I>^2 : 1.971 - <F>^2/ : 0.792 - <|E^2-1|> : 0.731 - <|L|>, : 0.484, 0.318 Multivariate Z score L-test: 1.741 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data are expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not necessarily exclude it. No (pseudo)merohedral twin laws were found. Patterson analyses - Largest peak height : 5.297 (corresponding p value : 0.86379) The largest off-origin peak in the Patterson function is 5.30% of the height of the origin peak. No significant pseudotranslation is detected. The results of the L-test indicate that the intensity statistics behave as expected. No twinning is suspected. ------------------------------------------------------------------------------- In this case, the only indicator for perfect twinning is 'Large values can indicate twinning, but small values do not necessarily exclude it.' ? --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D