[phenixbb] Problem starting TLS refinement

Pavel Afonine pafonine at lbl.gov
Fri May 16 11:19:46 PDT 2008

Hi Andrzej,

you are the first who's reporting TLS related error for the last few 
years, so this must be really weird.
To fix this problem and explain you what's wrong, I need to reproduce it 
myself on my computer.
Could you please send me (not to the whole bb) the PDB file or its 
fragment along with the exact command you use.

If you send the fragment of your PDB file, please make sure the error 
still happen.

As always, I will use your data for debugging only and I will discard it 
afterwards; I will keep it confidential.


On 5/16/2008 9:31 AM, Jendrek wrote:
> Hi,
>  I would like to do TLS but every time I try to start it I get 
> following error:
>   File 
> "/usr/local/cci_apps/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 
> "/usr/local/cci_apps-1421/cci_apps_sources/phenix/phenix/refinement/command_line.py", 
> line 69, in run
>     overwrite = command_line_interpreter.command_line.options.overwrite)
>   File 
> "/usr/local/cci_apps-1421/cci_apps_sources/phenix/phenix/refinement/driver.py", 
> line 199, in __init__
>     value          = 0.0)
>   File 
> "/usr/local/cci_apps-1421/cci_apps_sources/mmtbx/mmtbx/tls/tools.py", 
> line 735, in generate_tlsos
>     origins.append(xrs.center_of_mass())
>   File 
> "/usr/local/cci_apps-1421/cci_apps_sources/cctbx/cctbx/xray/structure.py", 
> line 943, in center_of_mass
>     return self.sites_cart().mean_weighted(weights=atomic_weights)
> RuntimeError: mean_weighted() argument is an empty array
>  I've attached my input file.
>  Any suggestions on what I'm doing wrong would be greatly appreciated.
>  Regards, Andrzej
> ------------------------------------------------------------------------
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