Re: [ccp4bb] Twin or underestimation of symmetry
This is a bit puzzling. Sticking to point groups: P3 P6 are sub groups of P6/mmm so data which merges in P6/mmm will always satisfy P3 and P6. And twinning in P3 or P6 will make the data seem to have higher symmetry. Four way twinning is unusual, but possible of course. But if you really have twinning, you should see it indicated in the pointless/aimless plots, or via Xtriage.. If those tests do not show it and you dont have a non-crystallographic translation twinning is unlikely. Your choice of SGs seem puzzling too. If the data is P31 (or P32) then you should see intensities for l=3n, and absences for l=3n+-1 If the data is P61 (or P65) then you should only see intensities for l=6n. If the data is P6322 you should only see intensities for l=2n. What are the absences along 00l? Eleanor On 29 July 2013 18:37, Jeffrey D Brodin jbro...@ucsd.edu wrote: Hi everyone, I have a dataset that's been giving me some trouble and wanted to get your ideas on the best way to proceed. The data extend to ~2.6 Å and scale integrate/scale well in P622. According to Pointless, the symmetry is either P622 or P6322, however, neither Molrep norm Phaser finds molecular replacement solutions in these space groups. If I run Phaser and let it check all other space groups it finds a solution in P6122, but I can only refine it to an Rfree value of ~35%. The data also scales well in P3 and P6 and I get molecular replacement solutions in space groups of either P31 or P61. However, the Refinement again stalls at an Rfree value of ~35%. I tried adding twin refinement in Refmac and it seems to be helping; The R/Rfree values dropped to 20.9/27.3 and the map appears much better compared to the previous refinements. The refined twin fractions are 0.26, 0.24, 0.24 and 0.25. Am I doing something wrong with the refinement or is this a legitimate way to treat the data. Thank you in advance for your help. * *
Re: [ccp4bb] Twin or underestimation of symmetry
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jeffrey, how complete is you model, i.e. what is the ratio between the number of atoms in the PDB file (without solvent/ ligands) and the expected number of atoms as calculated from the sequence? If a substantial part of the molecule is disordered you may not be able to get a much better model. What is the R-value and Rfree? If you have placed many water atoms you may have hovered out the difference density allowing you to further improve your model. Regards, Tim On 07/29/2013 07:37 PM, Jeffrey D Brodin wrote: Hi everyone, I have a dataset that's been giving me some trouble and wanted to get your ideas on the best way to proceed. The data extend to ~2.6 Å and scale integrate/scale well in P622. According to Pointless, the symmetry is either P622 or P6322, however, neither Molrep norm Phaser finds molecular replacement solutions in these space groups. If I run Phaser and let it check all other space groups it finds a solution in P6122, but I can only refine it to an Rfree value of ~35%. The data also scales well in P3 and P6 and I get molecular replacement solutions in space groups of either P31 or P61. However, the Refinement again stalls at an Rfree value of ~35%. I tried adding twin refinement in Refmac and it seems to be helping; The R/Rfree values dropped to 20.9/27.3 and the map appears much better compared to the previous refinements. The refined twin fractions are 0.26, 0.24, 0.24 and 0.25. Am I doing something wrong with the refinement or is this a legitimate way to treat the data. Thank you in advance for your help. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFR97DoUxlJ7aRr7hoRAsfrAKCIEYpOkrVfm/VrkIn+Jn9NZ16swACguGLe G1ZAwYDXmvyx/jK0iE7VjZo= =q8Ki -END PGP SIGNATURE-
Re: [ccp4bb] Twin or underestimation of symmetry
Check the pseudo-precession pics (0kl plane, etc). A rhombohedral crystal that is indexed as P6xx may have seemingly-bizarre systematic absences that could trick one into thinking its P63xx. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tim Gruene [t...@shelx.uni-ac.gwdg.de] Sent: Tuesday, July 30, 2013 7:26 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Twin or underestimation of symmetry -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jeffrey, how complete is you model, i.e. what is the ratio between the number of atoms in the PDB file (without solvent/ ligands) and the expected number of atoms as calculated from the sequence? If a substantial part of the molecule is disordered you may not be able to get a much better model. What is the R-value and Rfree? If you have placed many water atoms you may have hovered out the difference density allowing you to further improve your model. Regards, Tim On 07/29/2013 07:37 PM, Jeffrey D Brodin wrote: Hi everyone, I have a dataset that's been giving me some trouble and wanted to get your ideas on the best way to proceed. The data extend to ~2.6 Å and scale integrate/scale well in P622. According to Pointless, the symmetry is either P622 or P6322, however, neither Molrep norm Phaser finds molecular replacement solutions in these space groups. If I run Phaser and let it check all other space groups it finds a solution in P6122, but I can only refine it to an Rfree value of ~35%. The data also scales well in P3 and P6 and I get molecular replacement solutions in space groups of either P31 or P61. However, the Refinement again stalls at an Rfree value of ~35%. I tried adding twin refinement in Refmac and it seems to be helping; The R/Rfree values dropped to 20.9/27.3 and the map appears much better compared to the previous refinements. The refined twin fractions are 0.26, 0.24, 0.24 and 0.25. Am I doing something wrong with the refinement or is this a legitimate way to treat the data. Thank you in advance for your help. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFR97DoUxlJ7aRr7hoRAsfrAKCIEYpOkrVfm/VrkIn+Jn9NZ16swACguGLe G1ZAwYDXmvyx/jK0iE7VjZo= =q8Ki -END PGP SIGNATURE-
Re: [ccp4bb] Twin or underestimation of symmetry
The model is essentially 100% identical. The structure is of a point mutant that has already been solved. From: Tim Gruene [t...@shelx.uni-ac.gwdg.de] Sent: Tuesday, July 30, 2013 5:26 AM To: Jeffrey D Brodin Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Twin or underestimation of symmetry -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jeffrey, how complete is you model, i.e. what is the ratio between the number of atoms in the PDB file (without solvent/ ligands) and the expected number of atoms as calculated from the sequence? If a substantial part of the molecule is disordered you may not be able to get a much better model. What is the R-value and Rfree? If you have placed many water atoms you may have hovered out the difference density allowing you to further improve your model. Regards, Tim On 07/29/2013 07:37 PM, Jeffrey D Brodin wrote: Hi everyone, I have a dataset that's been giving me some trouble and wanted to get your ideas on the best way to proceed. The data extend to ~2.6 Å and scale integrate/scale well in P622. According to Pointless, the symmetry is either P622 or P6322, however, neither Molrep norm Phaser finds molecular replacement solutions in these space groups. If I run Phaser and let it check all other space groups it finds a solution in P6122, but I can only refine it to an Rfree value of ~35%. The data also scales well in P3 and P6 and I get molecular replacement solutions in space groups of either P31 or P61. However, the Refinement again stalls at an Rfree value of ~35%. I tried adding twin refinement in Refmac and it seems to be helping; The R/Rfree values dropped to 20.9/27.3 and the map appears much better compared to the previous refinements. The refined twin fractions are 0.26, 0.24, 0.24 and 0.25. Am I doing something wrong with the refinement or is this a legitimate way to treat the data. Thank you in advance for your help. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFR97DoUxlJ7aRr7hoRAsfrAKCIEYpOkrVfm/VrkIn+Jn9NZ16swACguGLe G1ZAwYDXmvyx/jK0iE7VjZo= =q8Ki -END PGP SIGNATURE-
[ccp4bb] Twin or underestimation of symmetry
Hi everyone, I have a dataset that's been giving me some trouble and wanted to get your ideas on the best way to proceed. The data extend to ~2.6 Å and scale integrate/scale well in P622. According to Pointless, the symmetry is either P622 or P6322, however, neither Molrep norm Phaser finds molecular replacement solutions in these space groups. If I run Phaser and let it check all other space groups it finds a solution in P6122, but I can only refine it to an Rfree value of ~35%. The data also scales well in P3 and P6 and I get molecular replacement solutions in space groups of either P31 or P61. However, the Refinement again stalls at an Rfree value of ~35%. I tried adding twin refinement in Refmac and it seems to be helping; The R/Rfree values dropped to 20.9/27.3 and the map appears much better compared to the previous refinements. The refined twin fractions are 0.26, 0.24, 0.24 and 0.25. Am I doing something wrong with the refinement or is this a legitimate way to treat the data. Thank you in advance for your help.
