Hi Pascal, the reason CNS tells you that there are no twin laws is that it only considers true merohedral twinning and not pseudo-merohedral - the latter is what xtriage is reporting. Cheers, Paul On Mar 1, 2008, at 4:04 PM, Pascal EGEA wrote:
Hi All
This a question of general Crystallography and use of Phenix to deal with twinned data.
I am having difficulties with a data set. We have data (2.6 ang resolution) that can be scaled and reduced in P222 with a Rmerge of 7%, the systematic absences show a screw axis ( it is P22(1)2). However MR in Phaser failed in this orthorhombic settings when searching for 2 molecules of the complex in the AU. If we reduce and scale the data in P2(1) and look at the diffraction pattern in HKLVIEW there is a /mmm symmetry. In the monoclinic P2(1) setting we can find 4 molecules of the complex (by MR in Phaser) and can refine it with Phenix to a Rfac/Rfree of 28%/ 34%. 2 molecules have good electron density whereas the two other ones have one of their domain very poorly defined in density. This is looking very suspicious to me and I am wondering if this refined structure is partially wrong?
Meanwhile I used phenix.triage on the data processed in P222 and I am confused with the output.
##----------------------------------------------------## ## Twinning Analyses ## ##----------------------------------------------------##
Using data between 10.00 to 3.36 Angstrom.
Determining possible twin laws.
The following twin laws have been found:
---------------------------------------------------------------------- --------- | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law | ---------------------------------------------------------------------- --------- | PM | 4-fold | 2.851 | 0.000 | 0.013 | -l,k,h | ---------------------------------------------------------------------- --------- M: Merohedral twin law PM: Pseudomerohedral twin law
0 merohedral twin operators found 1 pseudo-merohedral twin operators found In total, 1 twin operator were found
--------------------------------------------- Analysing possible twin law : -l,k,h ---------------------------------------------
Results of the H-test on acentric data:
(Only 50.0% of the strongest twin pairs were used)
mean |H| : 0.368 (0.50: untwinned; 0.0: 50% twinned) mean H^2 : 0.194 (0.33: untwinned; 0.0: 50% twinned) Estimation of twin fraction via mean |H|: 0.132 Estimation of twin fraction via cum. dist. of H: 0.115
Britton analyses
Extrapolation performed on 0.14 < alpha < 0.495 Estimated twin fraction: 0.127 Correlation: 0.9955
By comparison if I run the detect_twin routine of CNS it tells me that they are no merohedral twin laws for the point group 222 (using the statistical method of Yeates) ? This is confusing me quite a bit.
Assuming that the twinning law suggested by Phenix is correct how should I proceed? I have noticed the section concerning refinement using twinned data in Phenix phenix.refine data.hkl model.pdb twin_law="-k,-h,-l" detwin.map_types.aniso_correct=true
but It seems I only have a MR solution in P2(1) but not in P222(1) so how can I refine in P222(1)
I will greatly appreciate your input, many thanks.
Pascal F. Egea, PhD University of California San Francisco Department of Biophysics and Biochemistry Robert Stroud Laboratory [email protected]
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --