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
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
look.
Best wishes,
Graeme
On 11 February 2010 13:55, anon
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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
On Feb 11, 2010, at 5:55 AM, anon wrote:
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.
Graeme's answer is absolutely correct - Phenix doesn't handle unscaled data, and basically every program assumes that it has already been scaled and merged. (The partial exception: Scalepack files created with "no merge original index" can be used, but as far as I'm aware every program but SOLVE will merge the data internally. I'm not sure whether MOSFLM/SCALA/etc. can produce similar data, but I assume the same rules apply)
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; 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
To begin with, anything coming out of MOSFLM without scaling is going to be mangled - it isn't designed to deal with that kind of data. However, there is a secondary problem, which is that some columns that are created during data processing still cause problems even if you have scaled and merged data. Specifically, columns like M/ISYM are integers, and may differ between symmetry-related reflections. This causes problems during some of the internal transformations performed by the reflection file editor. The error message you should have seen was this:
"The data in
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)
You can't (this is deliberate - the complete job history information is used internally). You can flag individual jobs that you *do* want to see, and tell it to show only those jobs, or you can tell it not to display failed or aborted jobs - both of these mechanisms are intended as a substitute for deleting jobs. Nat ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
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Nathaniel Echols