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Hi Christopher,<br>
<br>
the error below looks like a bug. I would suggest getting the latest
phenix.refine (<i>Version 2007_04_26_2350</i>
) and I just verified that the commands "export_final_f_model=mtz"
and "export_final_f_model=cns" are working ok for this version.<br>
<br>
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.<br>
<br>
Please let me know if you have any questions.<br>
Thanks!<br>
Pavel.<br>
<br>
<br>
Rife, Christopher L wrote:
<blockquote
cite="mid35C208A168A04B4EB99D1E13F2A4DB01025EA8AA@exch-mail1.win.slac.stanford.edu"
type="cite">
<pre wrap="">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:
</pre>
<blockquote type="cite">
<pre wrap="">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'
</pre>
</blockquote>
<pre wrap=""><!---->
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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</pre>
</blockquote>
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