Dear phenix developers/users, I am using the phenix.refine and getting the error message: Traceback (most recent call last): File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/wxGUI2/Runtime.py", line 215, in OnComplete self.handle_complete_event(event) File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/wxGUI2/Programs/Refine/Output.py", line 130, in handle_complete_event refine_result = result) File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/wxGUI2/Programs/Refine/Output.py", line 180, in add_result_tabs self.add_validation_pages(refine_result) File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/wxGUI2/Programs/Validation/Results.py", line 57, in add_validation_pages seq_info=seq_info) File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/wxGUI2/Programs/Validation/Sequence.py", line 13, in __init__ Windows.AppPanel.__init__(self, parent) File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/wxGUI2/Windows.py", line 518, in __init__ WidgetArea.__init__(self, parent) File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/wxGUI2/Windows.py", line 479, in __init__ self.DisplayWidgets() File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/wxGUI2/Programs/Validation/Sequence.py", line 62, in DisplayWidgets table_data = self.seq_info.get_table_data() File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/cctbx_project/mmtbx/validation/sequence.py", line 320, in get_table_data table.extend(c.get_outliers_table()) TypeError: 'NoneType' object is not iterable I started 2 days ago, was running just fine last week. What should I do? Thanks in advance Filip

Ok thanks! Filip On 2012-07-16 14:43, Nathaniel Echols wrote:

On Mon, Jul 16, 2012 at 5:34 AM, Filip YABUKARSKI wrote:

...

Dear phenix developers/users,  I am using the phenix.refine and getting the error message:  File

"/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/cctbx_project/mmtbx/validation/sequence.py",

...

line 320, in get_table_data     table.extend(c.get_outliers_table()) TypeError: 'NoneType' object is not iterable

I started 2 days ago, was running just fine last week. What should  I do? Thanks in advance

Please update to the latest release (or nightly build).

-Nat

Links: ------ [1] mailto:[email protected]

Thanks, this helps a lot! On Jul 14, 2012, at 8:21 PM, Jeff Headd wrote:

Hi Yarrow,

Sorry for the confusion. If input intensities are used, then the French-Wilson method is used by default. If sigma_iobs_rejection_criteria is set to None as it is by default, then internally phenix.refine will set this value to -4 when using the F&W method. Having the value set to None by default allows us to use the sigma_iobs_rejection_criteria variable for both the F&W method and the old, simpler method, but each method needs a different default value, so the idea was to leave this is an internally determined parameter unless the user had good reason to change it otherwise.

I think we need to make this more clear. I'll see about adding a message to the log file that this change has occurred internally.

Since you've already used Truncate, you can tell phenix.refine to use your amplitude arrays as Fengyun suggested, or you can remove the intensity arrays from your input .mtz entirely using the reflection file editor.

Jeff

On Sat, Jul 14, 2012 at 8:01 PM, Yarrow Madrona wrote: Hi,

I recently noticed from reviewing the phenix.refine log file that phenix is scaling the input intensities using the French-Wilson Method. However, I have already run Truncate in CCP4 and have structure factors in my MTZ. So it appears that Phenix.refine ignores structure factors and uses intensities regardless.

The reason I am concerned is that Nat recently mentioned that the default for the sigma I cutoff is zero. However, The default in Truncate I thought was -3. If I understand correctly, the treatment in truncate allows weak reflections to be scaled and converted to structure factors. It seems that setting the I sigma cutoff to zero would cause you to loose some useable data. Currently, the sigma_fobs_rejection_criterion and sigma_ibos_rejection_criterion = None. This is the default I guess which would be 0. So my questions are:

1. Will setting:

sigma_iobs_rejection_criterion = -3

result in Phenix using a sigma I cutoff of -3?

2. How do I tell phenix to use the structure factors created by Truncate?

Thanks for your help. I apologize if I have some misconceptions as I am still relatively new to crystallography.

-Yarrow

-- Yarrow Madrona

Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb