Re: [ccp4bb] question about a dataset with pseudotranslational symmetry
Dear Jiyuan, you can use MOLREP which takes into account pseudotranslations. Good luck! Karsten > > Dear All, > > Recently I collected a data set to about 3.1 angstrom. Using Xtriage > program, I found a pseudo > translational symmetry on the c-axis. I noticed that overall diffraction > intensity is weak for this > dataset. I wonder if there are flaws in the crystal and I have difficulty > to solve the structure using > phaser. Has anyone seen similar cases and any comments and suggestions? > Thanks! > > Below is some analysis results from the Xtriage. > > Cell 102.937, 102.937, 203.059, 90, 90, 90, P422 > > - > Largest Patterson peak with length larger than 15 Angstrom > Frac. coord. : 0.000 0.000 0.350 > Distance to origin : 71.133 > Height (origin=100) : 48.451 > p_value(height) : 8.588e-05 > -- > Wilson ratio and moments > Acentric reflections > /^2 :2.568 (untwinned: 2.000; perfect twin 1.500) > ^2/ :0.728 (untwinned: 0.785; perfect twin 0.885) > <|E^2 - 1|> :0.850 (untwinned: 0.736; perfect twin 0.541) > Centric reflections > /^2 :3.953 (untwinned: 3.000; perfect twin 2.000) > ^2/ :0.577 (untwinned: 0.637; perfect twin 0.785) > <|E^2 - 1|> :1.111 (untwinned: 0.968; perfect twin 0.736) > > --- > NZ test (0<=z<1) to detect twinning and possible translational NCS > --- > | Z | Nac_obs | Nac_theo | Nc_obs | Nc_theo | > --- > | 0.0 | 0.000 | 0.000 | 0.000 | 0.000 | > | 0.1 | 0.126 | 0.095 | 0.293 | 0.248 | > | 0.2 | 0.239 | 0.181 | 0.394 | 0.345 | > | 0.3 | 0.327 | 0.259 | 0.471 | 0.419 | > | 0.4 | 0.401 | 0.330 | 0.521 | 0.474 | > | 0.5 | 0.464 | 0.394 | 0.557 | 0.520 | > | 0.6 | 0.518 | 0.451 | 0.597 | 0.561 | > | 0.7 | 0.569 | 0.503 | 0.635 | 0.597 | > | 0.8 | 0.613 | 0.551 | 0.660 | 0.629 | > | 0.9 | 0.648 | 0.593 | 0.683 | 0.657 | > | 1.0 | 0.679 | 0.632 | 0.706 | 0.683 | > --- > | Maximum deviation acentric : 0.071 | > | Maximum deviation centric : 0.052 | > | | > | _acentric : +0.054 | > | _centric : +0.035 | > > -- > L test for acentric data > using difference vectors (dh,dk,dl) of the form: > (2hp,2kp,3lp) > where hp, kp, and lp are random signed integers such that > 2 <= |dh| + |dk| + |dl| <= 8 > Mean |L| :0.490 (untwinned: 0.500; perfect twin: 0.375) > Mean L^2 :0.323 (untwinned: 0.333; perfect twin: 0.200) > The distribution of |L| values indicates a twin fraction of > 0.00. Note that this estimate is not as reliable as obtained > via a Britton plot or H-test if twin laws are available. > > --- > Twinning and intensity statistics summary (acentric data): > Statistics independent of twin laws > /^2 : 2.568 > ^2/ : 0.728 > <|E^2-1|> : 0.850 > <|L|>, : 0.490, 0.323 > Multivariate Z score L-test: 0.686 > > --- > > Jiyuan Ke, Ph.D. > Research Scientist > Van Andel Research Institute > 333 Bostwick Ave NE > Grand Rapids, MI 49503 > > --- Karsten Niefind University of Cologne Department of Chemistry Institute of Biochemistry Otto-Fischer-Str. 12-14 D-50674 Cologne Tel.: +49 221 470 6444 Fax: +49 221 470 3244
Re: [ccp4bb] question about a dataset with pseudotranslational symmetry
Hello, Which version of Phaser are you using ? As you must be aware, not all versions of Phaser deal in the most appropriate manner with cases of translational NCS if this is what you mean by "pseudo translational symmetry". Personally I'd go for the latest version of Phaser... HTH, Fred. > Message du 26/05/12 03:02 > De : "Ke, Jiyuan" > A : CCP4BB@JISCMAIL.AC.UK > Copie à : > Objet : [ccp4bb] question about a dataset with pseudotranslational symmetry > > Dear All, Recently I collected a data set to about 3.1 angstrom. Using Xtriage program, I found a pseudo translational symmetry on the c-axis. I noticed that overall diffraction intensity is weak for this dataset. I wonder if there are flaws in the crystal and I have difficulty to solve the structure using phaser. Has anyone seen similar cases and any comments and suggestions? Thanks! Below is some analysis results from the Xtriage. Cell 102.937, 102.937, 203.059, 90, 90, 90, P422 - Largest Patterson peak with length larger than 15 Angstrom Frac. coord. : 0.000 0.000 0.350 Distance to origin : 71.133 Height (origin=100) : 48.451 p_value(height) : 8.588e-05 -- Wilson ratio and moments Acentric reflections /^2 :2.568 (untwinned: 2.000; perfect twin 1.500) ^2/ :0.728 (untwinned: 0.785; perfect twin 0.885) :0.850 (untwinned: 0.736; perfect twin 0.541) Centric reflections /^2 :3.953 (untwinned: 3.000; perfect twin 2.000) ^2/ :0.577 (untwinned: 0.637; perfect twin 0.785) :1.111 (untwinned: 0.968; perfect twin 0.736) --- NZ test (0 --- | Z | Nac_obs | Nac_theo | Nc_obs | Nc_theo | --- | 0.0 | 0.000 | 0.000 | 0.000 | 0.000 | | 0.1 | 0.126 | 0.095 | 0.293 | 0.248 | | 0.2 | 0.239 | 0.181 | 0.394 | 0.345 | | 0.3 | 0.327 | 0.259 | 0.471 | 0.419 | | 0.4 | 0.401 | 0.330 | 0.521 | 0.474 | | 0.5 | 0.464 | 0.394 | 0.557 | 0.520 | | 0.6 | 0.518 | 0.451 | 0.597 | 0.561 | | 0.7 | 0.569 | 0.503 | 0.635 | 0.597 | | 0.8 | 0.613 | 0.551 | 0.660 | 0.629 | | 0.9 | 0.648 | 0.593 | 0.683 | 0.657 | | 1.0 | 0.679 | 0.632 | 0.706 | 0.683 | --- | Maximum deviation acentric : 0.071 | | Maximum deviation centric : 0.052 | | | | _acentric : +0.054 | | _centric : +0.035 | -- L test for acentric data using difference vectors (dh,dk,dl) of the form: (2hp,2kp,3lp) where hp, kp, and lp are random signed integers such that 2 Mean |L| :0.490 (untwinned: 0.500; perfect twin: 0.375) Mean L^2 :0.323 (untwinned: 0.333; perfect twin: 0.200) The distribution of |L| values indicates a twin fraction of 0.00. Note that this estimate is not as reliable as obtained via a Britton plot or H-test if twin laws are available. --- Twinning and intensity statistics summary (acentric data): Statistics independent of twin laws /^2 : 2.568 ^2/ : 0.728 : 0.850 , : 0.490, 0.323 Multivariate Z score L-test: 0.686 --- Jiyuan Ke, Ph.D. Research Scientist Van Andel Research Institute 333 Bostwick Ave NE Grand Rapids, MI 49503