[phenixbb] C2 twinning refinement

Peter Zwart PHZwart at lbl.gov
Sat Dec 13 13:06:18 PST 2008


Hi,

Thgis is very unfortunate. I have to provide a fix.

P


2008/12/12, whittle <whittle at mit.edu>:
> Hi all-
>
>  I'm hoping for some guidance on how to determine the correct twin law,
>  or possibly re-index my data to allow proper refinement.
>
>  The crystal appears to be R32, R3, or C2. Maps seem best in C2, even
>  though it merges equally well in all these spacegroup options, but R
>  stays high (~0.36/0.4) and a un-modelled helix visible in an untwinned
>  3.3 A dataset has no difference density in this set.
>
>  My attempt to treat the twinning have not worked (see output, including
>  cell dimensions, below).
>
>  Thanks in advance for any help!
>
>  James
>
>
>  phenix.xtriage flags it as most likely twinned with the following
>  output:
>
>  ...
>
>  Unit cell: (185.85, 120.972, 111.05, 90, 119.157, 90)
>  Space group: C 1 2 1 (No. 5)
>  Systematic absences: 0
>  Centric reflections: 1784
>  Resolution range: 28.8717 2.51224
>  Completeness in resolution range: 0.952773
>
>  ...
>
>  Using data between 10.00 to 3.24 Angstrom.
>
>  Determining possible twin laws.
>
>  The following twin laws have been found:
>
>  ----------------------------------------------------------------------------------------------------------------
>  | Type | Axis   | R metric (%) | delta (le Page) | delta (Lebedev) |
>  Twin law                                  |
>  ----------------------------------------------------------------------------------------------------------------
>  |  PM  | 2-fold | 0.345        | 0.219           | 0.003           |
>  -1/2*h+1/2*k+l,1/2*h-1/2*k+l,1/2*h+1/2*k  |
>  |  PM  | 2-fold | 0.345        | 0.219           | 0.003           |
>  -1/2*h-1/2*k+l,-1/2*h-1/2*k-l,1/2*h-1/2*k |
>  ----------------------------------------------------------------------------------------------------------------
>  M:  Merohedral twin law
>  PM: Pseudomerohedral twin law
>
>   0 merohedral twin operators found
>   2 pseudo-merohedral twin operators found
>  In total,   2 twin operator were found
>
>
>
>  The present crystal symmetry does not allow to have the its lattice
>  symmetry expressed in the setting desired.
>  Becasue of this, a full coset table cannot be produced. Working with the
>  data in the reduced cell will solve this.
>
>  Splitting data in centrics and acentrics
>   Number of centrics  : 961
>   Number of acentrics : 30683
>
>
>
>  phenix.refine with
>
>   twinning {
>     twin_law = "-1/2*h-1/2*k+l,-1/2*h-1/2*k-l,1/2*h-1/2*k"
>   }
>
>  results in the error:
>
>  Traceback (most recent call last):
>   File "/usr/local/phenix-1.3-
>  final/phenix/phenix/command_line/refine.py", line 5, in <module>
>     command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>   File "/usr/local/phenix-1.3-
>  final/phenix/phenix/refinement/command_line.py", line 89, in run
>     call_back_after_monitor_collect=call_back_after_monitor_collect)
>   File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/driver.py",
>  line 1081, in run
>     call_back_after_monitor_collect = call_back_after_monitor_collect)
>   File "/usr/local/phenix-1.3-
>  final/phenix/phenix/refinement/strategies.py", line 190, in
>  refinement_machine
>     twin_law = sgtbx.rt_mx( params.twinning.twin_law )
>  RuntimeError: cctbx Internal
>  Error: /net/anaconda/scratch1/phenix/phenix-1.3-
>  final/cctbx/sgtbx/rt_mx.cpp(230): Unsuitable value for rational rotation
>  matrix.
>
>
>
>
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>  phenixbb at phenix-online.org
>  http://www.phenix-online.org/mailman/listinfo/phenixbb
>


-- 
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P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
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