Opened 5 years ago

Closed 3 years ago

#3917 closed defect (fixed)

ISOLDE: get_symmetry_handler: structure is None

Reported by: s1960571@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-03-12)
Description
Tried to open ISOLDE after loading in a model. Got this:

chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE:
'Structure' object has no attribute '_ribbons_drawing'

File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/toolshed/info.py", line 627, in start_tool
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name, str(e)))

See log for complete Python traceback.


Log:
UCSF ChimeraX version: 0.93 (2020-03-12)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Downloading bundle ChimeraX_ISOLDE-1.0b5-cp37-cp37m-macosx_10_13_x86_64.whl  
Downloading bundle ChimeraX_ISOLDE-1.0b5-cp37-cp37m-macosx_10_13_x86_64.whl  
Error parsing
/Users/macbook/Downloads/ChimeraX_ISOLDE-1.0b5-cp37-cp37m-macosx_10_13_x86_64.whl:
No such file:
/Users/macbook/Downloads/ChimeraX_ISOLDE-1.0b5-cp37-cp37m-macosx_10_13_x86_64.whl  
File saved as
/Users/macbook/Downloads/ChimeraX_ISOLDE-1.0b5-cp37-cp37m-macosx_10_13_x86_64.whl  
Error parsing
/Users/macbook/Downloads/ChimeraX_ISOLDE-1.0b5-cp37-cp37m-macosx_10_13_x86_64.whl:
No such file:
/Users/macbook/Downloads/ChimeraX_ISOLDE-1.0b5-cp37-cp37m-macosx_10_13_x86_64.whl  
File saved as
/Users/macbook/Downloads/ChimeraX_ISOLDE-1.0b5-cp37-cp37m-macosx_10_13_x86_64.whl  
Downloading bundle ChimeraX_ISOLDE-1.0b5-cp37-cp37m-macosx_10_13_x86_64.whl  
Error parsing
/Users/macbook/Downloads/ChimeraX_ISOLDE-1.0b5-cp37-cp37m-macosx_10_13_x86_64.whl:
No such file:
/Users/macbook/Downloads/ChimeraX_ISOLDE-1.0b5-cp37-cp37m-macosx_10_13_x86_64.whl  
File saved as
/Users/macbook/Downloads/ChimeraX_ISOLDE-1.0b5-cp37-cp37m-macosx_10_13_x86_64.whl  
Downloading bundle ChimeraX_ISOLDE-1.0b5-cp37-cp37m-macosx_10_13_x86_64.whl  
Successfully installed ChimeraX-Clipper-0.12.1 ChimeraX-ISOLDE-1.0b5  
Installed ChimeraX-Clipper (0.12.1)  
Installed ChimeraX-ISOLDE (1.0b5)  

'clip' is a prefix of an existing command 'clipper'  

> toolshed show ISOLDE

> set selectionWidth 4

Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  
Traceback (most recent call last):  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1271, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1297, in add_xtal_data  
map_mgr = get_map_mgr(m, create=True, auto_add_to_session=True)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 174, in get_map_mgr  
sh = get_symmetry_handler(structure, create=create,
auto_add_to_session=auto_add_to_session)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 166, in _get_symmetry_handler  
p = structure.parent  
AttributeError: 'NoneType' object has no attribute 'parent'  
  
AttributeError: 'NoneType' object has no attribute 'parent'  
  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 166, in _get_symmetry_handler  
p = structure.parent  
  
See log for complete Python traceback.  
  

> open M60J

Missing filename suffix M60J  

> open 6M0J

Summary of feedback from opening 6M0J fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "NAG" near line 8378  
notes | Fetching compressed mmCIF 6m0j from
http://files.rcsb.org/download/6m0j.cif  
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif  
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif  
  
6m0j title:  
Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2
[more info...]  
  
Chain information for 6m0j #1  
---  
Chain | Description  
A | Angiotensin-converting enzyme 2  
E | Spike receptor binding domain  
  
Non-standard residues in 6m0j #1  
---  
CL — chloride ion  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
ZN — zinc ion  
  
  

> toolshed show ISOLDE

> set selectionWidth 4

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 621, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1612, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/__init__.py", line 128, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tools.py", line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/tool.py", line 184, in __init__  
self.isolde = isolde.Isolde(self)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 312, in __init__  
self._start_gui(gui)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 456, in _start_gui  
self._populate_menus_and_update_params()  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 557, in
_populate_menus_and_update_params  
self._update_model_list(None, None, force=True)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1023, in _update_model_list  
self._change_selected_model(model=current_model)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2460, in _change_selected_model  
sh = get_symmetry_handler(m, create=True, auto_add_to_session=True)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 564, in __init__  
spotlight_mode=spotlight_mode)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 608, in add_model  
self.atomic_symmetry_model  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 850, in atomic_symmetry_model  
return AtomicSymmetryModel(self, self.spotlight_radius,
live=self.spotlight_mode, debug=self._debug)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1198, in __init__  
self, dim_colors_to)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1809, in __init__  
_copy_ribbon_drawing(self.master_ribbon, self, dim_factor)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1818, in master_ribbon  
return self.structure._ribbons_drawing  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute '_ribbons_drawing'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1361, in <lambda>  
run(ses, "toolshed show %s" % StringArg.unparse(tool_name)))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 339, in toolshed_show  
bi.start_tool(session, name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
'Structure' object has no attribute '_ribbons_drawing'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
'Structure' object has no attribute '_ribbons_drawing'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  

> open 6M0J format mmCIF fromDatabase pdb

Summary of feedback from opening 6M0J fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "NAG" near line 8378  
  
6m0j title:  
Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2
[more info...]  
  
Chain information for 6m0j #1  
---  
Chain | Description  
A | Angiotensin-converting enzyme 2  
E | Spike receptor binding domain  
  
Non-standard residues in 6m0j #1  
---  
CL — chloride ion  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
ZN — zinc ion  
  
  
'ISOLDE_ToolUI' object has no attribute 'isolde'  

> toolshed show ISOLDE

> set selectionWidth 4

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 621, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1612, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/__init__.py", line 128, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tools.py", line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/tool.py", line 184, in __init__  
self.isolde = isolde.Isolde(self)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 312, in __init__  
self._start_gui(gui)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 456, in _start_gui  
self._populate_menus_and_update_params()  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 557, in
_populate_menus_and_update_params  
self._update_model_list(None, None, force=True)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1023, in _update_model_list  
self._change_selected_model(model=current_model)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2460, in _change_selected_model  
sh = get_symmetry_handler(m, create=True, auto_add_to_session=True)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 564, in __init__  
spotlight_mode=spotlight_mode)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 608, in add_model  
self.atomic_symmetry_model  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 850, in atomic_symmetry_model  
return AtomicSymmetryModel(self, self.spotlight_radius,
live=self.spotlight_mode, debug=self._debug)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1198, in __init__  
self, dim_colors_to)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1809, in __init__  
_copy_ribbon_drawing(self.master_ribbon, self, dim_factor)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1818, in master_ribbon  
return self.structure._ribbons_drawing  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute '_ribbons_drawing'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1361, in <lambda>  
run(ses, "toolshed show %s" % StringArg.unparse(tool_name)))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 339, in toolshed_show  
bi.start_tool(session, name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
'Structure' object has no attribute '_ribbons_drawing'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
'Structure' object has no attribute '_ribbons_drawing'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  
'ISOLDE_ToolUI' object has no attribute 'isolde'  

> open 6M0J format mmCIF fromDatabase pdb

Summary of feedback from opening 6M0J fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "NAG" near line 8378  
  
6m0j title:  
Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2
[more info...]  
  
Chain information for 6m0j #1  
---  
Chain | Description  
A | Angiotensin-converting enzyme 2  
E | Spike receptor binding domain  
  
Non-standard residues in 6m0j #1  
---  
CL — chloride ion  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
ZN — zinc ion  
  
  

> toolshed show ISOLDE

> set selectionWidth 4

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 621, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1612, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/__init__.py", line 128, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tools.py", line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/tool.py", line 184, in __init__  
self.isolde = isolde.Isolde(self)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 312, in __init__  
self._start_gui(gui)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 456, in _start_gui  
self._populate_menus_and_update_params()  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 557, in
_populate_menus_and_update_params  
self._update_model_list(None, None, force=True)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1023, in _update_model_list  
self._change_selected_model(model=current_model)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2460, in _change_selected_model  
sh = get_symmetry_handler(m, create=True, auto_add_to_session=True)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 564, in __init__  
spotlight_mode=spotlight_mode)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 608, in add_model  
self.atomic_symmetry_model  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 850, in atomic_symmetry_model  
return AtomicSymmetryModel(self, self.spotlight_radius,
live=self.spotlight_mode, debug=self._debug)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1198, in __init__  
self, dim_colors_to)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1809, in __init__  
_copy_ribbon_drawing(self.master_ribbon, self, dim_factor)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1818, in master_ribbon  
return self.structure._ribbons_drawing  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute '_ribbons_drawing'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1361, in <lambda>  
run(ses, "toolshed show %s" % StringArg.unparse(tool_name)))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 339, in toolshed_show  
bi.start_tool(session, name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
'Structure' object has no attribute '_ribbons_drawing'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
'Structure' object has no attribute '_ribbons_drawing'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  

> open 1HHO format mmCIF fromDatabase pdb

1hho title:  
Structure of human oxyhaemoglobin At 2.1 angstroms resolution [more info...]  
  
Chain information for 1hho #1  
---  
Chain | Description  
A | hemoglobin A (oxy) (α chain)  
B | hemoglobin A (oxy) (β chain)  
  
Non-standard residues in 1hho #1  
---  
HEM — protoporphyrin IX containing Fe (HEME)  
OXY — oxygen molecule  
PO4 — phosphate ion  
  
1hho mmCIF Assemblies  
---  
1| author_defined_assembly  
  
  
'ISOLDE_ToolUI' object has no attribute 'isolde'  

> toolshed show ISOLDE

> set selectionWidth 4

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 621, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1612, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/__init__.py", line 128, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tools.py", line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/tool.py", line 184, in __init__  
self.isolde = isolde.Isolde(self)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 312, in __init__  
self._start_gui(gui)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 456, in _start_gui  
self._populate_menus_and_update_params()  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 557, in
_populate_menus_and_update_params  
self._update_model_list(None, None, force=True)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1023, in _update_model_list  
self._change_selected_model(model=current_model)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2460, in _change_selected_model  
sh = get_symmetry_handler(m, create=True, auto_add_to_session=True)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 564, in __init__  
spotlight_mode=spotlight_mode)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 608, in add_model  
self.atomic_symmetry_model  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 850, in atomic_symmetry_model  
return AtomicSymmetryModel(self, self.spotlight_radius,
live=self.spotlight_mode, debug=self._debug)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1198, in __init__  
self, dim_colors_to)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1809, in __init__  
_copy_ribbon_drawing(self.master_ribbon, self, dim_factor)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1818, in master_ribbon  
return self.structure._ribbons_drawing  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute '_ribbons_drawing'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1361, in <lambda>  
run(ses, "toolshed show %s" % StringArg.unparse(tool_name)))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 339, in toolshed_show  
bi.start_tool(session, name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
'Structure' object has no attribute '_ribbons_drawing'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
'Structure' object has no attribute '_ribbons_drawing'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  
'ISOLDE_ToolUI' object has no attribute 'isolde'  

> open 6M0J format mmCIF fromDatabase pdb

Summary of feedback from opening 6M0J fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "NAG" near line 8378  
  
6m0j title:  
Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2
[more info...]  
  
Chain information for 6m0j #1  
---  
Chain | Description  
A | Angiotensin-converting enzyme 2  
E | Spike receptor binding domain  
  
Non-standard residues in 6m0j #1  
---  
CL — chloride ion  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
ZN — zinc ion  
  
  

> toolshed show ISOLDE

> set selectionWidth 4

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 621, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1612, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/__init__.py", line 128, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tools.py", line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/tool.py", line 184, in __init__  
self.isolde = isolde.Isolde(self)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 312, in __init__  
self._start_gui(gui)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 456, in _start_gui  
self._populate_menus_and_update_params()  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 557, in
_populate_menus_and_update_params  
self._update_model_list(None, None, force=True)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1023, in _update_model_list  
self._change_selected_model(model=current_model)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2460, in _change_selected_model  
sh = get_symmetry_handler(m, create=True, auto_add_to_session=True)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 564, in __init__  
spotlight_mode=spotlight_mode)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 608, in add_model  
self.atomic_symmetry_model  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 850, in atomic_symmetry_model  
return AtomicSymmetryModel(self, self.spotlight_radius,
live=self.spotlight_mode, debug=self._debug)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1198, in __init__  
self, dim_colors_to)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1809, in __init__  
_copy_ribbon_drawing(self.master_ribbon, self, dim_factor)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1818, in master_ribbon  
return self.structure._ribbons_drawing  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute '_ribbons_drawing'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1361, in <lambda>  
run(ses, "toolshed show %s" % StringArg.unparse(tool_name)))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 339, in toolshed_show  
bi.start_tool(session, name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
'Structure' object has no attribute '_ribbons_drawing'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
'Structure' object has no attribute '_ribbons_drawing'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  
'ISOLDE_ToolUI' object has no attribute 'isolde'  

> open "/Users/macbook/Desktop/Assignements and course documents/Year 2/TDC
> 2/Assessed exercise/Section 4/XDATA.pdb"

XDATA.pdb title:  
Crystal structure of sars-cov-2 spike receptor-binding domain bound with ACE2
[more info...]  
  
Chain information for XDATA.pdb #1  
---  
Chain | Description  
A | angiotensin-converting enzyme 2  
E | spike receptor binding domain  
  
Non-standard residues in XDATA.pdb #1  
---  
CL — chloride ion  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
ZN — zinc ion  
  

> toolshed show ISOLDE

> set selectionWidth 4

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 621, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1612, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/__init__.py", line 128, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tools.py", line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/tool.py", line 184, in __init__  
self.isolde = isolde.Isolde(self)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 312, in __init__  
self._start_gui(gui)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 456, in _start_gui  
self._populate_menus_and_update_params()  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 557, in
_populate_menus_and_update_params  
self._update_model_list(None, None, force=True)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1023, in _update_model_list  
self._change_selected_model(model=current_model)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2460, in _change_selected_model  
sh = get_symmetry_handler(m, create=True, auto_add_to_session=True)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 564, in __init__  
spotlight_mode=spotlight_mode)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 608, in add_model  
self.atomic_symmetry_model  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 850, in atomic_symmetry_model  
return AtomicSymmetryModel(self, self.spotlight_radius,
live=self.spotlight_mode, debug=self._debug)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1198, in __init__  
self, dim_colors_to)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1809, in __init__  
_copy_ribbon_drawing(self.master_ribbon, self, dim_factor)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1818, in master_ribbon  
return self.structure._ribbons_drawing  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute '_ribbons_drawing'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1361, in <lambda>  
run(ses, "toolshed show %s" % StringArg.unparse(tool_name)))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 339, in toolshed_show  
bi.start_tool(session, name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
'Structure' object has no attribute '_ribbons_drawing'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
'Structure' object has no attribute '_ribbons_drawing'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  
'ISOLDE_ToolUI' object has no attribute 'isolde'  

> open "/Users/macbook/Desktop/Assignements and course documents/Year 2/TDC
> 2/Assessed exercise/Section 4/XDATA.pdb"

XDATA.pdb title:  
Crystal structure of sars-cov-2 spike receptor-binding domain bound with ACE2
[more info...]  
  
Chain information for XDATA.pdb #1  
---  
Chain | Description  
A | angiotensin-converting enzyme 2  
E | spike receptor binding domain  
  
Non-standard residues in XDATA.pdb #1  
---  
CL — chloride ion  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
ZN — zinc ion  
  

> show atoms

> hide cartoons

> toolshed show ISOLDE

> set selectionWidth 4

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 621, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1612, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/__init__.py", line 128, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tools.py", line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/tool.py", line 184, in __init__  
self.isolde = isolde.Isolde(self)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 312, in __init__  
self._start_gui(gui)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 456, in _start_gui  
self._populate_menus_and_update_params()  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 557, in
_populate_menus_and_update_params  
self._update_model_list(None, None, force=True)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1023, in _update_model_list  
self._change_selected_model(model=current_model)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2460, in _change_selected_model  
sh = get_symmetry_handler(m, create=True, auto_add_to_session=True)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 564, in __init__  
spotlight_mode=spotlight_mode)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 608, in add_model  
self.atomic_symmetry_model  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 850, in atomic_symmetry_model  
return AtomicSymmetryModel(self, self.spotlight_radius,
live=self.spotlight_mode, debug=self._debug)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1198, in __init__  
self, dim_colors_to)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1809, in __init__  
_copy_ribbon_drawing(self.master_ribbon, self, dim_factor)  
File "/Users/macbook/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/clipper/symmetry.py", line 1818, in master_ribbon  
return self.structure._ribbons_drawing  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute '_ribbons_drawing'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1361, in <lambda>  
run(ses, "toolshed show %s" % StringArg.unparse(tool_name)))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 339, in toolshed_show  
bi.start_tool(session, name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
'Structure' object has no attribute '_ribbons_drawing'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
'Structure' object has no attribute '_ribbons_drawing'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel Inc.

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: get_symmetry_handler: structure is None

comment:2 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed

Clearing out the backlog of fixed-but-unclosed tickets.

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