Hi Dirk, Nice cross validation flags for twin refinement do obey the twin law: if (h,k,l) is in the free set, then (k, h, -l) should be as well. Same is/should be true for work set btw.
In phenix, we generate test reflections that follow the lattice symmetry (*). This means that even if you do not realise that your data is potentially twinned (or has a wrong point group), you do not end up biasing your test set. The actual reductionof a low symmetry free set to high symmetry free set is a bit of 'art- and fly-work' (kunst en vliegwerk) , but is doable. The CNS "make_cv_twin.inp" script needs a specific twin law. In the case where more then a single twin law is possible, taking them all into account is not a bad idea. Cheers Peter (*) check out: http://phenix-online.org/cctbx_sources/cctbx/cctbx/miller.py and look for the function def denerate_r_free_flags_on_lattice_symmetry 2007/10/23, Dirk Kostrewa <[EMAIL PROTECTED]>: > Hi John, > > if I understand the "make_cv_twin.inp" correctly, then this script takes > care about separating reflections related by the twin law to avoid a > potential bias of the Free-R set with twin-law-related reflections from the > working set. At least, in the source of this script I read the comment: "{- > make sure all twin related reflections are in the same set -}". If this is > true, then you simply don't have to worry any further about your good > R-factors, but enjoy a very well refined structure! > Maybe, the authors of this CNS script could comment on this separation of > reflections? > > Best regards, > > Dirk. > > > Am 23.10.2007 um 15:32 schrieb john kryst: > > Hi CCP4bb , > > Thanks for your suggestions... here is the summary of the > structure... > > I am working in deletion and point mutants. I have a mutant (P61 resoln > 3.1A) with partial twinning with twinning fraction 0.28. Wilson b-factor is > 50. The data collected in the home source with normal exposure time. The > rmsd's of the refined structure is 0.0081 (bonds) and 1.38672 (angles). > Molprobity is score is 50 without any manual model building (just after the > refinement). > > Since the structure is twinned new free R-flag has been chosen according to > CNS make_cv_twin.inp. The b-factor has been flattened to 30. Then > rigid-body_twin refinement followed by simulated annealing_twin is done > (heating the structure up to 5000K with different initial velocity trials). > The R and R free after this step is 18.35 and 27.22. Then i did > bgroup_twin refinement which gave me R and R free 17.06 25.63. Further > model building and refinement tend to reduce the R and Rfee upto 15 and 23. > > I deleted some portion of the molecule and did refinement. But proper > density appeared after it. > > Please help me out. > > John > > > > ******************************************************* > Dirk Kostrewa > Gene Center, A 5.07 > Ludwig-Maximilians-University > Feodor-Lynen-Str. 25 > 81377 Munich > Germany > Phone: +49-89-2180-76845 > Fax: +49-89-2180-76999 > E-mail: [EMAIL PROTECTED] > ******************************************************* > >
