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