[phenixbb] Reflection output

Pavel Afonine PAfonine at lbl.gov
Wed May 9 12:16:22 PDT 2007

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.

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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20070509/5ade19c0/attachment-0004.htm>

More information about the phenixbb mailing list