Dumb question here: When one runs the various twinning tests (e.g. phenix.xtriage), is one meant to use data processed in the higher symmetry SG, or the lower symmetry SG? A concrete example: I can process a data set in a 622 point group w/ reasonable merging statistics, but an abnormally low solvent content raises my suspicions. So do I process as P6, and submit these data to the twinning test? Or do I submit the data processed as P622? Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 [email protected]
P6
You may also want to process in P1. xtriage will then try all possible
subgroups of P622.
Ralf
On Thu, Apr 19, 2012 at 9:45 AM, Patrick Loll
Dumb question here: When one runs the various twinning tests (e.g. phenix.xtriage), is one meant to use data processed in the higher symmetry SG, or the lower symmetry SG?
A concrete example: I can process a data set in a 622 point group w/ reasonable merging statistics, but an abnormally low solvent content raises my suspicions. So do I process as P6, and submit these data to the twinning test? Or do I submit the data processed as P622?
Pat
--------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA
(215) 762-7706 [email protected]
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Pat, As Ralf says, P6 or P1. I think if the data merges well in both P622 and P6 then you are going to get very similar twinning statistics in the two space groups. This would not be true if the data merged poorly in P622; in that case merging to P622 it would make it look twinned. All the best, Tom T ________________________________________ From: [email protected] [[email protected]] on behalf of Patrick Loll [[email protected]] Sent: Thursday, April 19, 2012 10:45 AM To: PHENIX user mailing list Subject: [phenixbb] twinning question Dumb question here: When one runs the various twinning tests (e.g. phenix.xtriage), is one meant to use data processed in the higher symmetry SG, or the lower symmetry SG? A concrete example: I can process a data set in a 622 point group w/ reasonable merging statistics, but an abnormally low solvent content raises my suspicions. So do I process as P6, and submit these data to the twinning test? Or do I submit the data processed as P622? Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 [email protected] _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
IMHO. if you have P622 apparent symmetry, your true symmetry could be either P6, P321, P312, or if you are unlucky, it is P3 and there are 4 twin domains. So the others are possibly right in suggesting P1 for twinning tests. BW, Gabor On Apr 19 2012, Patrick Loll wrote:
Dumb question here: When one runs the various twinning tests (e.g. phenix.xtriage), is one meant to use data processed in the higher symmetry SG, or the lower symmetry SG?
A concrete example: I can process a data set in a 622 point group w/ reasonable merging statistics, but an abnormally low solvent content raises my suspicions. So do I process as P6, and submit these data to the twinning test? Or do I submit the data processed as P622?
Pat
--------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA
(215) 762-7706 [email protected]
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- ################################################## Dr Gabor Bunkoczi Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 0XY ##################################################
Did I infer correctly from Padilla & Yeates (2002) Acta Cryst D59:1124-30
that the L-test could indicate twinning even if data were merged in the
apparent higher-symmetry point group?
Wolfram Tempel
On Thu, Apr 19, 2012 at 12:45 PM, Patrick Loll
Dumb question here: When one runs the various twinning tests (e.g. phenix.xtriage), is one meant to use data processed in the higher symmetry SG, or the lower symmetry SG?
A concrete example: I can process a data set in a 622 point group w/ reasonable merging statistics, but an abnormally low solvent content raises my suspicions. So do I process as P6, and submit these data to the twinning test? Or do I submit the data processed as P622?
Pat
--------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA
(215) 762-7706 [email protected]
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
The effects of twinning on the intensity distributions should be seen in even the highest point group. However, there won't be twin laws to test for twinning (and hence twin fraction estimation). For a more complete analysis looking at the data processed in the lower symmetry (P6 or below) would be better. On Apr 20, 2012, at 8:42 AM, wtempel wrote:
Did I infer correctly from Padilla & Yeates (2002) Acta Cryst D59:1124-30 that the L-test could indicate twinning even if data were merged in the apparent higher-symmetry point group? Wolfram Tempel
On Thu, Apr 19, 2012 at 12:45 PM, Patrick Loll
wrote: Dumb question here: When one runs the various twinning tests (e.g. phenix.xtriage), is one meant to use data processed in the higher symmetry SG, or the lower symmetry SG? A concrete example: I can process a data set in a 622 point group w/ reasonable merging statistics, but an abnormally low solvent content raises my suspicions. So do I process as P6, and submit these data to the twinning test? Or do I submit the data processed as P622?
Pat
--------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA
(215) 762-7706 [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
-- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ [email protected] ][ 1-510-495-2506 ] --
participants (6)
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Gabor Bunkoczi
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Patrick Loll
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Paul Adams
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Ralf Grosse-Kunstleve
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Terwilliger, Thomas C
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wtempel