Clipper: name '_f_sigf_chooser' is not defined

[jared.sampson@…]

The following bug report has been submitted:
Platform:        Darwin-16.7.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-12-17)
Description
1. Load a phenix-output model.  
2. Open Isolde. 
3. Click "Load crystallographic dataset"

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.8 (2018-12-17)  
How to cite UCSF ChimeraX  
Updating list of available bundles failed: 'list' object has no attribute
'split'  

> cd ~/projects/vrc42/refine_uca_complex/4_phenix

Current working directory is:
/Users/jared/Dropbox/Projects/vrc42/refine_uca_complex/4_phenix  

> open
/Users/jared/Dropbox/Projects/vrc42/refine_uca_complex/4_phenix/4_phenix_001.pdb

Summary of feedback from opening
/Users/jared/Dropbox/Projects/vrc42/refine_uca_complex/4_phenix/4_phenix_001.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2019-05-01 Time 13:11:08 EDT -0400 (1556730668.19 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name : ../VRC42UCA_refine_19.mtz  
  
76 messages similar to the above omitted  
  
Chain information for 4_phenix_001.pdb #1  
---  
Chain | Description  
A L | No description available  
B H | No description available  
C T | No description available  
  

> toolshed show ISOLDE

Chain information for 4_phenix_001.pdb  
---  
Chain | Description  
1.3/A 1.3/L | No description available  
1.3/B 1.3/H | No description available  
1.3/C 1.3/T | No description available  
  
Traceback (most recent call last):  
File "/Users/jared/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 1179, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/Users/jared/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 1206, in add_xtal_data  
xmapset = map_mgr.add_xmapset_from_mtz(filename, self.params.map_shannon_rate)  
File "/Users/jared/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/map_mgr.py", line 239, in add_xmapset_from_mtz  
return XmapSet(self, mtzdata)  
File "/Users/jared/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/xmapset.py", line 169, in __init__  
choice = self._choose_fsigf(crystal_data)  
File "/Users/jared/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/xmapset.py", line 453, in _choose_fsigf  
choice = _f_sigf_chooser(list(fsigfs.keys()))  
NameError: name '_f_sigf_chooser' is not defined  
  
NameError: name '_f_sigf_chooser' is not defined  
  
File "/Users/jared/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/xmapset.py", line 453, in _choose_fsigf  
choice = _f_sigf_chooser(list(fsigfs.keys()))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-10.25.22
OpenGL renderer: Intel(R) Iris(TM) Graphics 540
OpenGL vendor: Intel Inc.

[tic20@…]

Oops! My bad. The Clipper plugin currently only allows you to use one set of F/sigF data at a time. If you load a MTZ file with more than one it *should* bring up a dialog box allowing you to choose the one you want, but I clearly messed it up. For now, the easiest thing is to make a reduced MTZ file with just the data you want ISOLDE to see. I’ll get a proper fix in by the next release (towards the end of this month).
 

 

[jared.sampson@…]

Great! Thanks for the quick reply.  

I'll plan to make a modified MTZ for now and then look forward to the fix in the next release.

Best,
Jared


On May 6, 2019 at 2:59:01 PM, ChimeraX (chimerax-bugs-admin@cgl.ucsf.edu) wrote:

#1913: Clipper: name '_f_sigf_chooser' is not defined
--------------------------------------+----------------------
Reporter: jared.sampson@… | Owner: tic20
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------------+----------------------

Comment (by tic20@…):

{{{
Oops! My bad. The Clipper plugin currently only allows you to use one set
of F/sigF data at a time. If you load a MTZ file with more than one it
*should* bring up a dialog box allowing you to choose the one you want,
but I clearly messed it up. For now, the easiest thing is to make a
reduced MTZ file with just the data you want ISOLDE to see. I’ll get a
proper fix in by the next release (towards the end of this month).





}}}

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1913#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Tristan Croll]

The current release no longer raises an error when there is more than one reflection dataset in the file - but doesn't let you choose either. The automatic choice is (merged intensities > anomalous intensities > merged amplitudes > anomalous amplitudes), considering only the first of each type. The next ISOLDE release will bring up a window allowing you to specify exactly which set you want when loading via its "Load crystallographic dataset" button. Loading via the command line (i.e. "open xxx.mtz structureModel #1" or "open xxxx structureFactors true") will still use the automatic choice mechanism.