[phenixbb] error: running phenix.refine

Pavel Afonine PAfonine at lbl.gov
Wed Sep 16 21:31:45 PDT 2009


Hi Ravi,

- version 1.3 is old and it is the best to try one of the latest ones:

http://www.phenix-online.org/download/nightly_builds.cgi

- if you get the same error using the latest installer, I will need to 
see the inputs you used: data file, command line parameters. It would be 
helpful if you send me those.

Pavel.




On 9/16/09 8:04 PM, RAVINDRA D MAKDE wrote:
> Hello all,
>
> I will greatly appreciate the help for the following:
>
> I am getting the error "RuntimeError: min() argument is an empty 
> array" (more details error message given below) while running 
> phenix.refine. I am using PHENIX:  Version: 1.3 on  Platform: 
> mac-intel-osx osx-10.5.7
>
> My error message is as follows: 
>
> 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 68, in run
>     log=log)
>   File 
> "/usr/local/phenix-1.3-final/phenix/phenix/refinement/command_line.py", 
> line 231, in __init__
>     reflection_file_server = self.reflection_file_server()
>   File 
> "/usr/local/phenix-1.3-final/phenix/phenix/refinement/command_line.py", 
> line 566, in reflection_file_server
>     err=self.log)
>   File 
> "/usr/local/phenix-1.3-final/iotbx/iotbx/reflection_file_utils.py", 
> line 379, in __init__
>     force_symmetry=self.force_symmetry))
>   File 
> "/usr/local/phenix-1.3-final/iotbx/iotbx/reflection_file_reader.py", 
> line 197, in as_miller_arrays
>     base_array_info=base_array_info)
>   File "/usr/local/phenix-1.3-final/iotbx/iotbx/mtz/__init__.py", line 
> 424, in as_miller_arrays
>     and flex.min(column_group.sigmas()) > 0):
> *RuntimeError: min() argument is an empty array*
>
>
> Thanks in advance,
>
> Regards,
>
> Ravi
>
>
> Ravindra D. Makde, PhD
> Postdoctoral fellow, Tan lab,
> The Department of Biochemistry and Molecular Biology,
> The Pennsylvania State University,
> University Park, PA 16802
> USA
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>   
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20090916/f19a1634/attachment-0003.htm>


More information about the phenixbb mailing list