[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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>
--
-----------------------------------------------------------------
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
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX: http://cctbx.sf.net
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