Thank you for cell. For P32 21 2 spacegroup with this cell the only higher Laue symmetry you could generate is P6/mmm, so as Jonathan says I wouldnt worry about the FreeR assignment.. I can look at possible NCS operators if you like - the most informative output is to run MOLREP Self Rotation on your data.. And maybe PISA on the coordinates to see what sort of assembly it suggests.. Eleanor
On Tue, 16 Jun 2020 at 01:29, Jonathan Cooper < 00000c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote: > I remember we discussed this a lot about a year ago when Ed Berry revived > a thread from 2003! > > > https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind1905&L=CCP4BB&O=D&P=72099 > > I think the upshot of it all was that you do not need to use shells even > with quite high NCS since Ian Tickle rightly persuaded us that over-fitting > is due to measurement errors and there is no reason to expect these to be > correlated for NCS-related reflections. However, as you have probably found > out by now, you can make an R-free set in shells using the reflection file > editor in phenix. From memory you may also need to make sure that you use a > CCP4-style R-free flag (i.e. the free-set reflections should be flagged > zero) if you are going to use Refmac. There's a screenshot here: > > http://u.cubeupload.com/jbcooper/202006160114071280x8.png > > Hope this helps! > On Monday, 15 June 2020, 17:42:15 BST, Eleanor Dodson < > 0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > > > Hmm - this finally was rather deprecated - there are some less happy > consequences to have all reflections in a particular resolution shell > excluded. > If your NCS means there is pseudo- symmetry in the diffraction and it > would be possible to have a cell with higher point symmetry (an example > might be be Pmmm or P4mm if a(Pmmm) ~ b(Pmmmm). ) then you could assign > freer flags in the higher symmetry group and extend then to the lower... > > What is your cell, and do you know the NCS operators? > Eleanor > > > On Mon, 15 Jun 2020 at 16:54, <Shymaa Damfo> <shymaa.damfo...@ucl.ac.uk> > wrote: > > Hello, > > I'm refining protein structure in Refmac and I have NCS greater than 4 ( > I've 8 identical subunits in the asymmetric unit). > > In the "Refinement parameters" section in Refmac, how can I pick Rfree set > based on thin resolution shells rather than in the normal random method? > > I've read about the program "dataman" from the usf suite which could help > with this but found it very complicated. > > Do you have any advice to solve this? or would you recommend any other > program? > > > Thank you in advance > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
