Sudipta, keep in mind that programs that detect twinning (like Xtriage) estimate twin fraction, while refinement programs (like Refmac, phenix.refine and others) actually refine twin fraction. This is why a discrepancy between estimated twin fraction and refined one should not terribly surprise you!
POLYGON (http://www.phenix-online.org/papers/lv5003_reprint.pdf) is the tool designed to answer questions like yours #5 . All the best, Pavel On Wed, Sep 17, 2014 at 11:23 PM, Sudipta Bhattacharyya < sudiptabhattacharyya.iit...@gmail.com> wrote: > Dear Community, > > Recently, we could solve a structure of DNA/protein complex through MR > phasing. The data was initially indexed and scaled in P622 space group, > however owing to the incompatibility of a single DNA/protein complex to fit > in the ASU, it could not be solved in that space group (according to > solvent content analysis). Since it was an indication of possible twining > event, we tried MR in P321, P312 and P6 space groups respectively and > finally got a very good solution in P65. According to phenix xtriage > analysis, the data may be a near perfect merohedrally twinned one (twining > fraction 0.425, Britton analysis; 0.468 H test; 0.478 ML method; with a > possible twin operator h,-h-k,-l), however, the L test rather suggest no > such twining event (but the graph of acentric observed, appeared slightly, > sigmoidal compared to the straight acentric theoretical in the L test). The > same phenomenon happened when we checked the data for possible twining in > Truncate (twin fraction: L test: No; H test, 0.42, Murray Rust, 0.35; > Britton ML, 0.47; possible twin operator: h+k,-k,-l). On the other hand, > while refining the data in Refmac5 with intensity based twin option ON, > Refmac5 suggested a perfect merohedral twining with the fraction of > 0.49/0.50. > > In the context of these confusing situation, now my questions are - > > 1. Is the data twinned or not? > 2. With such a high twining fraction, is it solvable? > 3. What refinement programs will be the best choices for refinement of > such a twinned data? > 4. In one of the tutorials of Refmac5 it has been suggested, in such twin > refinement cases, to choose Rfree set in higher space group (in our case > P6522) then expand it to lower space group (in our case P65), could anybody > please let me know how to do that in CCP4 or else? > 5. It is a data of 4A resolution could anyone tell me what final R/Rfree > one could expect from a 4A data (although it may sound a dumb question...) > > Any help will be highly appreciated. > > With my best regards, > Sudipta. > > Sudipta Bhattacharyya, > Postdoctoral Research Fellow, > Colorado State University, Fort Collins, > Colorado, USA. > > > >
