[phenixbb] Reflection output

Rife, Christopher L crife at slac.stanford.edu
Wed May 9 11:13:58 PDT 2007


Hi,

In trying to get a reflection file written out after refinement with phenix.refine (version 2007_03_13_2155), we found a couple of problems.

1. The documentation gives the example of including "export_final_f_model=mtz" in the command line input, however, phenix complains that it does not know this command. It is possible to work around this by changing "write_refined_fmodel_to_file" in the param file to true. 

2. When the model is refined with twinning, trying to write out the reflection file causes it to crash with the following error:

> Writing refined fmodel to plain text file:
>   /data5/Completed/PH10062D-47717/Phenix/model_001_fmodel.hkl
> Traceback (most recent call last):
>   File
> "/home/sdcsoftware/linux/cci_apps_sources/phenix/phenix/comman
> d_line/refine.py", line 5, in <module>
>     command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>   File
> "/home/sdcsoftware/linux/cci_apps_sources/phenix/phenix/refine
> ment/command_line.py", line 86, in run
>     if(output.write_refined_fmodel_to_file): 
> refine_object.write_refined_fmodel(f_hkl)
>   File
> "/home/sdcsoftware/linux/cci_apps_sources/phenix/phenix/refine
> ment/driver.py", line 927, in write_refined_fmodel
>     self.fmodel.dump(out = f)
> AttributeError: 'twin_model_manager' object has no attribute 'dump'

We are trying to prepare files for deposition, so any assistance would be welcome.

Thanks,
Chris

-----------------------------------------
Structure Determination Core
Joint Center for Structural Genomics
Stanford Synchrotron Radiation Laboratory




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