Hi Christopher,

the error below looks like a bug. I would suggest getting the latest phenix.refine (Version 2007_04_26_2350 ) and I just verified that the commands "export_final_f_model=mtz" and "export_final_f_model=cns" are working ok for this version.

However, there is still problem with using  export_final_f_model command in twin refinement. This will be fixed for the next versions. For the moment please don't use export_final_f_model in twin refinement to avoid program crash.

Please let me know if you have any questions.
Thanks!
Pavel.


Rife, Christopher L wrote: 
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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