[phenixbb] twinning analysis

Peter Zwart PHZwart at lbl.gov
Wed Apr 23 09:47:51 PDT 2008


Hi,

this is a bug that has been fixed in an upcomming release.

Short of an easy fix, try running phenix.refine with the twin law
given by xtriage. There should only be a single on.

P

2008/4/23, Andreas Förster <docandreas at gmail.com>:
> Hey all,
>
>  I've been digging around with a nasty dataset for a while, twinning,
>  pseudosymmetry, etc.  Phenix.xtriage has helped me make some guesses as
>  to what's going on, but phenix.twin_map_utils fails.  I used an mtz file
>  obtained from XDS via f2mtz and cad as xray data, like so:
>
>  phenix.twin_map_utils xray_data.file=blah.mtz model=blah.pdb
>  unit_cell=86.623,86.623,121.357,90,90,120 space_group=P65
>
>  Here's the error:
>
>  Traceback (most recent call last):
>    File
>  "/usr/local/2008_02_08_1610/cci_apps_sources/mmtbx/mmtbx/command_line/twin_map_utils.py",
>
>  line 7, in <module>
>      twin_map_utils.run(args=sys.argv[1:])
>    File
>  "/usr/local/2008_02_08_1610/cci_apps_sources/mmtbx/mmtbx/twinning/twin_map_utils.py",
>
>  line 256, in run
>      tmp_params = utils.r_free_flags_params.extract()
>  AttributeError: 'module' object has no attribute 'r_free_flags_params'
>
>
>  I see the error on a recent macbook pro with current cci_apps.  How can
>  I get around it?
>
>  Thanks
>
>
>  Andreas
>
>
>  ps. I apologize if that question posted to the board earlier.  I wrote
>  from a wrong account.
>  _______________________________________________
>  phenixbb mailing list
>  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
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