[phenixbb] phenix.refine crash
Pavel Afonine
pafonine at lbl.gov
Sat Feb 24 21:40:12 PST 2007
Hi,
this is known problem and it will be fixed ASAP; sorry for this.
This presumably happens because an atom selected to be refined as
individual anisotropic is included into a TLS group.
I will let you know once the fixed version of CCI Apps is available.
Pavel.
Jianghai Zhu wrote:
> Hi,
>
> I was using phenix.refine from the latest cci apps bundle to do
> tls+individual_sites+individual_adp refinement. The program crashed
> with the following error message.
>
> ----------Target weights (before refinement)----------
>
>
> Traceback (most recent call last):
> File
> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/command_line/refine.py",
> line 5, in <module>
> command_line.run(command_name="phenix.refine", args=sys.argv[1:])
> File
> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/command_line.py",
> line 75, in run
> call_back_after_monitor_collect=call_back_after_monitor_collect)
> File
> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/driver.py",
> line 1108, in run
> log = log)
> File
> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/strategies.py",
> line 245, in refinement_machine
> log = log)
> File
> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/weight_xray_chem.py",
> line 222, in __init__
> compute_gradients = True)
> File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/restraints.py",
> line 144, in energies_adp_aniso
> xray_structure = xray_structure,
> File
> "/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py",
> line 109, in __init__
> self.check_flags(fl_i)
> File
> "/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py",
> line 177, in check_flags
> assert not fl.use_u_aniso()
> AssertionError
>
> Anyone has any idea what is happening? Thanks.
>
> Jianghai
>
> +++++++++++++++++++++++++++++++
> Jianghai Zhu, Ph.D
> CBR Institute for Biomedical Research
> Department of Pathology
> Harvard Medical School
> 200 Longwood Ave., Boston, MA 02115
> Ph: 617-278-3211
> Fx: 618-278-3232
> +++++++++++++++++++++++++++++++
>
>
>
> ------------------------------------------------------------------------
>
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> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
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