[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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