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How have you assigned the Free R set? If there is twinning you need to make sure that the related reflections have the same FreeR assignment. This is now standard in the new FreeR software written by Ville, and called from GUI2, but it used to require some jiggery poky to achieve. Next question - are you sure of the spacegroup? Obviously absences in an I-centred spacegroup cannot indicate whether it is I222 or I21 21 21 Eleanor On 2 March 2017 at 06:30, Robbie Joosten <[log in to unmask]> wrote: > Hi Alun and Kay, > > > > PDB_REDO does some more extended twinning testing with among others > Phaser, so it would be worthwhile to have a look at that. On the server it > refuses to do twinned refinement if there is no clear indication of > twinning even if the user assumed twinning before. > > The fact the R-free does nothing, but R goes down using the twin target > suggests me that there is more going on in the refinement. Perhaps you > should look at optimising other refinement parameters* > > > > Cheers, > > Robbie > > > > *e.g. with The pdb-redo webserver 😉 > > > > Sent from my Windows 10 phone > > > > *Van: *Kay Diederichs <[log in to unmask]> > *Verzonden: *woensdag 1 maart 2017 23:38 > *Aan: *[log in to unmask] > *Onderwerp: *Re: [ccp4bb] Twinning and R-Free > > > Hi Alun, > > that's difficult to understand for me. It is my understanding that for an > imperfect model, refmac will indicate a twin fraction >0 even if in reality > it is 0. But alpha=0.372 sounds too high for that. > My questions would be - > a) is it a single dataset, or did you merge ? If the latter, it might just > be a problem of alternative indexing. > b) PDB_REDO uses refmac AFAIK so the result should not be different from > when _you_ run refmac? > c) the spacegroup is I4 but twinning makes it appear close to I422? > d) what exactly are the aimless statistics you refer to? what exactly does > pointless report? > e) could it be a data processing problem? Crummy data often look twinned > just because errors are interpreted as twinning. > > best, > Kay > > > > On Wed, 1 Mar 2017 22:03:07 +0000, Alun R Coker <[log in to unmask]> > wrote: > > >Hi Everyone, > > > >I have a (2.5 - 2.3 Angstroms) data set the process as I4 or I222. > >Aimless indicates twinning in both space groups and all the lower > >symmetry space groups consistent with the reduced cell. Molecular > >replacement works in I4 but not I222 etc. I can see new density for a > >ligand we are interested in some of the 6 subunits so all seems > >promising. I've refined in refmac without the twinning turned on in > >order to avoid model bias and end up with an R-factor/R-free of > >0.268/0.305. However, if I repeat the last round of refinement with > >twinning turned on the R-factor drops but not the R-free (R/R-free > >0.237/0.305). Remac reckons the twin fraction is 0.628/0.372. > > > >My question is does the drop in R-factor but not R-free suggest I am > >over-fitting the model by refining twinning? > > > >Running the data and model through pdb redo suggest the data isn't > twinned. > > > >Thanks, > > > >Alun > > > >-- > >Dr Alun R. Coker > >Senior Lecturer > >Wolfson Institute for Biomedical Research > >University College London > >The Cruciform Building > >London > >WC1E 6BT > > > >Tel: 020 7679 6703 Ext 46703 > >Web: www.ucl.ac.uk/pxmed >