[phenixbb] Reflection output

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


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.


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

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