[phenixbb] iMosflm .mtz

Graeme Winter graeme.winter at googlemail.com
Thu Feb 11 06:02:02 PST 2010

Dear Anon,

The data need to be scaled before they can be used in downstream
analysis, so exactly as you have found it is necessary to run Scala on
the measurements before running Autosol.

Although the output format from iMosflm is MTZ, the column structure
is not what phenix expects - as much as anything, the partial
measurements from adjacent images have not been combined.

You will probably find if you want to get in to Phenix quickly that
taking the MTZ from iMosflm and running pointless and Scala with the
defaults will do a reasonable job, though the output from both are
very helpful and informative and your time is well spent taking a

Best wishes,


On 11 February 2010 13:55, anon <phenix.ccp4 at googlemail.com> wrote:
> Hi,
> i was under the impression Phenix (AutoSol) could handle .mtz files from
> iMosflm, however when i input the .mtz file into AutoSol, no labels appears
> in the pull-down menu, and pressing Run results in a dialogue box appearing
> stating you must select a column label for the reflection file, if no labels
> are present it may not be a valid format.
> If i input the iMosflm .mtz file into phenix.reflection_file_editor, and
> copy over the I, SIGI, M_ISYM columns, i get the following error;
> A Python error was detected.  This is probably a bug; click "OK" to send a
> bug report to the PHENIX developers.
> TypeError : not all arguments converted during string formatting
> Traceback (most recent call last):
>   File "/usr/local/phenix-1.6-289/phenix/wxGUI2/MainWindow.py", line 880, in
> OnRun
>     self.run()
>   File "/usr/local/phenix-1.6-289/phenix/wxGUI2/Programs/HKLTools.py", line
> 81, in run
>     symmetry_callback=None) # TODO
>   File
> "/usr/local/phenix-1.6-289/cctbx_project/iotbx/reflection_file_editor.py",
> line 358, in __init__
>     "related reflections are not identical.)" % array_name)
> TypeError: not all arguments converted during string formatting
> When i use the scaled .mtz file produced by scala, AutoSol works fine. Just
> wondering what's going on!
> Also, how do you delete individual Jobs in the Job History window (ie jobs
> that have failed or you no longer want to keep  etc)
> Thanks for the help
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