[phenixbb] problem with a twinned data set
Peter Zwart
PHZwart at lbl.gov
Sun Mar 2 03:44:58 PST 2008
2008/3/2, Randy J. Read <rjr27 at cam.ac.uk>:
> In addition to what has been suggested, another option is to merge the data
> in P1 and look for 8 copies. Now that you have a reasonable refined model
> from the monoclinic solution, this should find a solution. Then you can
> look for the symmetry in the molecular replacement solution to decide what
> symmetry is crystallographic. An easy shortcut is to run a self-rotation
> function on the Fcalcs from the model. (At the moment, I think you'll have
> to go outside Phenix to do that -- we're intending to put a self-rotation
> function into Phaser but it's still on the to-do list!)
Actually, you can run xtriage on your calculated data and get merging
stats for crystallographic sym. ops. : much easier to interpret
ascompared to a self rotation (and done for you!).
Alternatively, you can get aproximate operators using
phenix.simple_ncs_from_pdb. This might bit prove a bit of a hassle
though.
hth
P
> Regards
>
>
> Randy Read
>
>
> On Mar 2 2008, 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
> >pascal at msg.ucsf.edu
> >
> >
> >
> >
>
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