[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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>   
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