ISOLDE: name '_f_sigf_chooser' is not defined

[ash@…]

The following bug report has been submitted:
Platform:        Linux-4.15.0-48-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.8 (2018-12-17)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | Traceback (most recent call last):  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
self.init_available_from_cache(logger)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 445, in  
init_available_from_cache  
abc.load_from_cache()  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 61, in load_from_cache  
b = _build_bundle(d)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 242, in _build_bundle  
keywords = _extract_extra_keywords(keywords)  
File "/opt/bioxray/programs/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/installed.py", line 270, in  
_extract_extra_keywords  
all_kwds = [k.strip() for k in kwds.split(',')]  
AttributeError: 'list' object has no attribute 'split'  
  
UCSF ChimeraX version: 0.8 (2018-12-17)  
How to cite UCSF ChimeraX  

> toolshed show ISOLDE

> open /u/azsha/AS/CVI03/Buster/LoopC_test_120819/refine_all_140819.pdb

Summary of feedback from opening
/u/azsha/AS/CVI03/Buster/LoopC_test_120819/refine_all_140819.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK --------------------- added by autoBUSTER
-------------------------------  
  
Ignored bad PDB record found on line 2  
REMARK run at = Mon Aug 12 10:28:08 CEST 2019  
  
Ignored bad PDB record found on line 14  
REMARK Files used:  
  
Ignored bad PDB record found on line 15  
REMARK PDB = /u/azsha/AS/CVI03/Buster/LoopC_test_120819/pdbchk.pd  
  
Ignored bad PDB record found on line 16  
REMARK MTZ = /u/azsha/AS/CVI03/090819/xscale_CVI03Sy7_merged_p21_  
  
45 messages similar to the above omitted  
  
Chain information for refine_all_140819.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
Chain information for refine_all_140819.pdb  
---  
Chain | Description  
1.3/A | No description available  
1.3/B | No description available  
1.3/C | No description available  
  

> toolshed show ISOLDE

Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 1179, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/u/azsha/.local/share/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 "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/map_mgr.py", line 239, in add_xmapset_from_mtz  
return XmapSet(self, mtzdata)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/xmapset.py", line 169, in __init__  
choice = self._choose_fsigf(crystal_data)  
File "/u/azsha/.local/share/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 "/u/azsha/.local/share/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.  
  
Traceback (most recent call last):  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 1179, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/u/azsha/.local/share/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 "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/map_mgr.py", line 239, in add_xmapset_from_mtz  
return XmapSet(self, mtzdata)  
File "/u/azsha/.local/share/ChimeraX/0.8/site-
packages/chimerax/clipper/maps/xmapset.py", line 169, in __init__  
choice = self._choose_fsigf(crystal_data)  
File "/u/azsha/.local/share/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 "/u/azsha/.local/share/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: 3.3.0 NVIDIA 418.40.04
OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tristan Croll]

My bad. This is an error in 1.0b2 that comes up if your input MTZ file has more than one F/sigF array in it. It's fixed in the latest development versions (just download the latest ChimeraX daily and install ISOLDE via the ToolShed as normal), or you can avoid it by using an external editor to trim down your file to just the F/sigF array you want.

I would *strongly* advise updating in any case - ChimeraX 0.8 and the associated ISOLDE are quite ancient now.