[phenixbb] problem with a twinned data set
Pascal EGEA
pascal at msg.ucsf.edu
Sat Mar 1 16:04:39 PST 2008
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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