Hi Keller, I do not how to check twin fraction after Refmac (I guess it's somewhere in log file). From the log file it seems I have four twin domain:
Twin operators with estimated twin fractions **** Twin operator: H, K, L: Fraction = 0.275; Equivalent operators: K, -H-K, L; -H-K, H, L Twin operator: -K, -H, -L: Fraction = 0.228; Equivalent operators: -H, H+K, -L; H+K, -K, -L Twin operator: K, H, -L: Fraction = 0.270; Equivalent operators: H, -H-K, -L; -H-K, K, -L Twin operator: -H, -K, L: Fraction = 0.228; Equivalent operators: -K, H+K, L; H+K, -H, L On Thu, Apr 13, 2017 at 4:36 PM, Keller, Jacob <kell...@janelia.hhmi.org> wrote: > What was the refined twin fraction after Refmac? It’s much more accurate > than initial tests. Also, how many twin domains do you have? If you have > many, it might be a higher space group but with less twinning. I recently > had a case in which apparent tetartohedral (four-domain) twinning in P32 > was really hemihedral (two-domain) twinning in P3212: > > > > *Acta Cryst. <http://journals.iucr.org/d>* (2017). D*73* > <http://journals.iucr.org/d/contents/backissues.html>, 22-31 > https://doi.org/10.1107/S2059798316019318 > > > > Jacob > > > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of > *Eleanor > Dodson > *Sent:* Thursday, April 13, 2017 3:11 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] Refmac5 twin refinement pushing Rfree > surprisingly down > > > > Twin refinement cannot be compared directly to untwinned - the R factors > are between different parameters - without twinning it is assumed you have > an amplitude obtained more or less from sqrt(I But for a twinned data set > that I is actually [ I1 + twin_factor I2 ] so the amplitude is not really > correct and twinned refinement will give a much better estimate. > > > > However you need to be careful that you have assigned the same FreeR flag > to reflection pair related by the twin law. The modern program in the CCP4 > data reduction pipeline looks after this pretty automatically - all > possible symmetry equivalents are assigned the same FreeR but older > software did not do this.. > > > > You can check it by looking at some twin equivalents - in SG P32 these > could be h k l and -h, -k, l or h k l and k h -l or h k l and -k, -h, -l . > > > > Ideally they all should have the same Free R flag.. > > > > Eleanor > > > > PS - the acid test is: Do the maps look better? > > > > E > > > > > > On 13 April 2017 at 19:52, Robbie Joosten <r.joos...@nki.nl> wrote: > > Hi Alex, > > > > You are not giving the number after refinement without the twin > refinement. Nevertheless, R-free drops like this are not unheard of. You > should check your Refmac log file, it would warn you of potential space > group errors. Refmac will also give you a refined estimate of the twin > fraction. > > > > Cheers, > > Robbie > > > > Sent from my Windows 10 phone > > > > *Van: *Alex Lee <alexlee198...@gmail.com> > *Verzonden: *donderdag 13 april 2017 19:19 > *Aan: *CCP4BB@JISCMAIL.AC.UK > *Onderwerp: *[ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly > down > > > > Dear All, > > > > I have a protein/dna complex crystal and data collected at 3A and another > set at 2.8A, space group P32. L test shows twinning (fraction around 0.11). > The structure solved by MR and model building of the complex finish (no > solvent built yet, I do not think it's good to build solvent in such low > resolution data). > > > > I did Refmac5 to refine my structure (restraint refinement) with or > without twinning, to my surprise, the Rfree drops a lot after twin > refinement of two data sets. Summary below: > > > > 2.8A dataset: before twin refine 34%, 29%; after twin refine:24%, 19% > > 3A dataset: before twin refine 30%;26%; after refine 25%, 18% > > > > I know that a lot of threads in CCP4bb talking about Rfree after twin > refine and Rfree without twin refine can not compare directly. By drop R > free this much by twin refine, it gives me a feeling of too good to be true > (at such low resolution with such good Rfree, maybe overrefined a lot?), > but from the density map after twin refine, it does seem better than no > twin refine map. > > > > I do not know if reviewers are going to challenge this part. > > > > Any input is appreciated. > > > > > > > > >
