Hi Jürgen, in phenix.refine I would do:
phenix.refine [PDB] [mtz] twin_law="h,-k,-l" main.ncs=true ncs.type=torsion (or equivalent using the GUI). Note, "ncs.type=torsion" will use the new NCS handling machinery that takes care of NCS automatically with no need the user to provide definitions for NCS groups. For this it is advisable to use a recent Phenix version from the nightly builds. If resolution is ~3-2.8A and higher, then automated water update using ordered_solvent=true is good to use, so no need to waste time doing it manually. If it is a final refinement run before PDB deposition then weights optimization using optimize_xyz_weight=true and optimize_adp_weight=true should be tried. That's all I can tell given the information you provided. All the best, Pavel On Tue, Mar 27, 2012 at 1:37 PM, Bosch, Juergen <[email protected]> wrote: > Dear CCP4BBers and PhenixBBers (cross posting here, since we all read both > anyhow) > > to the experts out there here's my question: > > We have a P21 dataset with 2 molecules in the asu and a refined twin > fraction of 38% according to phenix.refine using a twin law operator. > > My gut feeling tells me that I can't use NCS unless I detwin the data, is > that a correct assumption ? > > How does phenix.refine [PDB] [mtz] twin_law="h,-k,-l" main_ncs=true would > deal with this problem ? > > Same question goes to Garib, it's very convenient to just specify twin in > your Refmac script without further values and magic happens but what if I > add NCS restrains, will Refmac treat them correctly according to the twin > operator ? > > Twins are confusing in real life and even more in crystals I think. > > And no the data can not be processed in a higher space group, P222 results > in Rmerges of >40% in the lowest resolution shell, the beta angle is 92.4 > degrees in P21. And if processed in P1 we get 4 molecules per asu and a > refined twin fraction of 50%, which in my eyes clearly indicates it's not > P1 but really P21. > > Hope to get some interesting feedback on this issue. > > Thanks, > > Jürgen > > ...................... > Jürgen Bosch > Johns Hopkins University > Bloomberg School of Public Health > Department of Biochemistry & Molecular Biology > Johns Hopkins Malaria Research Institute > 615 North Wolfe Street, W8708 > Baltimore, MD 21205 > Office: +1-410-614-4742 > Lab: +1-410-614-4894 > Fax: +1-410-955-2926 > http://web.mac.com/bosch_lab/ > > > > >
