Hi One way to test if the data processing software has imposed too much symmetry is to actually look at the images themselves using one of the processing packages, or process in a lower symmetry and use "viewhkl" (or even "hklview" if you're old-fashioned...) to view sections of the integrated data down principal axes. The human eye/brain combination takes a lot of beating.
Harry On 3 Apr 2019, at 11:03, herman.schreu...@sanofi.com wrote: > I agree. The data processing software might have been confused by the NC > 2-fold and thought that it was crystallographic and of course, after merging > the data, the NC axis will have been made “crystallographic” with > superimposed A and B conformations at 50% occupancy. In this case, > reprocessing in the true, lower symmetry space group, would bring better > stats, but also much clearer and much easier interpretable electron density > maps. However, if the distribution of you’re A and B conformations is truly > random you could submit the structure as it is now. > Best, Herman > > Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von David > Briggs > Gesendet: Mittwoch, 3. April 2019 10:46 > An: CCP4BB@JISCMAIL.AC.UK > Betreff: [EXTERNAL] Re: [ccp4bb] pseudo internal symmetry > > Hi, > > This doesn't answer your question directly, but I'd be tempted to reduce the > symmetry and re-refine in a space group lacking that 2-fold axis. > I'd hope that the scaling in the lower space group would give you better > stats as well, but maybe the differences in your case are too subtle? > > I don't know what PDB rules and regs are though. > > HTH, > > Dave > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Daniele de > Sanctis <de.sanct...@gmail.com> > Sent: 03 April 2019 09:36 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] pseudo internal symmetry > > Hi all, > > we have a structure with a pseudo internal symmetry along a 2-fold axis that > sits on a 2-fold crystallographic axis. For refinement purposes we have > modeled the parts that differ with 50% occupancy, but before depositing the > structure we wanted to make sure that this is the best way to deal with it > and it is in agreement with PDB standards. > > Did anyone deal with similar cases in the past? > > Cheers > > Daniele > > > -- > > ἀρετή > --------------------------------------- > Daniele de Sanctis > Structural Biology Group > ESRF - The European Synchrotron > Grenoble, France > Tel 33 (0)4 76 88 2869 > > http://www.esrf.eu/id29 > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > The Francis Crick Institute Limited is a registered charity in England and > Wales no. 1140062 and a company registered in England and Wales no. 06885462, > with its registered office at 1 Midland Road London NW1 1AT > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
