[phenixbb] Reflection output
PAfonine at lbl.gov
Wed May 9 12:16:22 PDT 2007
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
Please let me know if you have any questions.
Rife, Christopher L wrote:
> 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:
>> Traceback (most recent call last):
>> d_line/refine.py", line 5, in <module>
>> command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>> ment/command_line.py", line 86, in run
>> 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
> phenixbb mailing list
> phenixbb at phenix-online.org
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