[phenixbb] Error in the end of phenix-refine with NCS

[José Trincão]

Hi, these were run in separate directories (to different resolutions). I am running again with and without real-space refinement.
Somehow I always get strange python errors when using the gui, so I am running everything from command line.
Thanks

Jose

On Apr 22, 2010, at 22/4/10 - 16:12, Pavel Afonine wrote:

Hi José,

the error is very weird... Could it be that while refinement was running you deleted some files that phenix.refine created at the start? Can you try running this refinement again in empty directory?
Are you using the GUI or command line?

Pavel.

On 4/22/10 3:47 AM, José Trincão wrote:
> Hello,
> I ran 2 jobs of phenix.refine with ncs (disabled automatic definition) and real-space refinement, weight optimization, 3 macrocycles. In the end of the third macrocycle I got these error messages for both:
> ===================== NCS restraints at end of refinement =====================
> 
> NCS restraint group 1:
>  NCS operator 1:
>    Reference selection: "chain A"
>        Other selection: "chain B"
>    Number of atom pairs: 9281
> Traceback (most recent call last):
>  File "/usr/local/phenix-1.6.1-357/phenix/phenix/command_line/refine.py", line 11, in <module>
>    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>  File "/usr/local/phenix-1.6.1-357/phenix/phenix/refinement/command_line.py", line 89, in run
>    call_back_handler=call_back_handler)
>  File "/usr/local/phenix-1.6.1-357/phenix/phenix/refinement/driver.py", line 1187, in run
>    out        = log)
>  File "/usr/local/phenix-1.6.1-357/cctbx_project/mmtbx/ncs/restraints.py", line 713, in show_operators
>    ncs_operators.show(sites_cart=sites_cart, out=out, prefix=prefix+"  ")
>  File "/usr/local/phenix-1.6.1-357/cctbx_project/mmtbx/ncs/restraints.py", line 470, in show
>    prefix=prefix+"  ")
>  File "/usr/local/phenix-1.6.1-357/cctbx_project/libtbx/utils.py", line 690, in write
>    file_object.write(str)
> IOError: [Errno 5] Input/output error
> 
> What could be the problem?
> 
> Thanks.
> 
> Jose
> 
> 
> José Trincão, PhD	CQFB at FCT-UNL
> 2829-516 Caparica, Portugal
> 
> "It's very hard to make predictions... especially about the future" - Niels Bohr
> 
> 
> 
> 
> 
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José Trincão, PhD	CQFB at FCT-UNL
2829-516 Caparica, Portugal

"It's very hard to make predictions... especially about the future" - Niels Bohr