[phenixbb] problem with a twinned data set
Peter Zwart
PHZwart at lbl.gov
Sat Mar 1 16:25:21 PST 2008
Hi Pascal,
A couple of points.
1. If you cannot find an MR solution in P222 but you can in P2 pg's,
try pg P2. Twin law you have to use is missing two fold along a,b or
c.
2. Equivalent to the four-fold pseudo merohedral twinlaw you mention,
is the two fold 'k,h,-l'. Use that one instead when trying to refine
in pg p222. This is a bug/feature in phenix.xtriage. It is a pseudo
merohedral twin law and you will not find it in merohedral lookup
tables (which is why we don't use lookup tables).
3. When 'true' poing group is P2, there are 3 possible P2's you have
to try. When indexing in LABELIT, MOSFLM or D*TREK, you will have
three unique monoclinic choices (rather then a single one). You should
try all.
4. For the P222 case, make sure you don't bite yourself in the neck by
assuming specific absences / spacegroups. Try all! When 'absent data'
is twinned with 'non absent data', one can be easily fooled.
HTH
Peter
2008/3/1, Pascal EGEA <pascal at msg.ucsf.edu>:
>
> 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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