close tool → 'MainWindow' object has no attribute '_hide_tools_shown_states'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.0.0-25-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.91 (2019-10-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | could not retrieve bundle list from toolshed  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.91 (2019-10-03)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> show target ab

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> color sel bynucleotide

> toolshed show Toolbar

Downloading bundle ChimeraX_ISOLDE-1.0b3.dev5-cp37-cp37m-linux_x86_64.whl  
Successfully installed ChimeraX-Clipper-0.9.9 ChimeraX-ISOLDE-1.0b3.dev5  
Installed ChimeraX-Clipper (0.9.9)  
Installed ChimeraX-ISOLDE (1.0b3.dev5)  

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

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1811, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 552, in close_request  
tool_instance.delete()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/help_viewer/tool.py", line 370, in delete  
ToolInstance.delete(self)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/tools.py", line 175, in delete  
self.session.ui.remove_tool(self)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 294, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 689, in remove_tool  
tw._destroy()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1716, in _destroy  
self.__toolkit.destroy()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1838, in destroy  
self.main_window._tool_window_destroyed(self.tool_window)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1500, in _tool_window_destroyed  
if tool_window in self._hide_tools_shown_states:  
AttributeError: 'MainWindow' object has no attribute
'_hide_tools_shown_states'  
  
AttributeError: 'MainWindow' object has no attribute
'_hide_tools_shown_states'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1500, in _tool_window_destroyed  
if tool_window in self._hide_tools_shown_states:  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1811, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 548, in close_request  
is_main_window = tool_window is all_windows[0]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 548, in close_request  
is_main_window = tool_window is all_windows[0]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1811, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 552, in close_request  
tool_instance.delete()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/tools.py", line 175, in delete  
self.session.ui.remove_tool(self)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 294, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 689, in remove_tool  
tw._destroy()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1716, in _destroy  
self.__toolkit.destroy()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1838, in destroy  
self.main_window._tool_window_destroyed(self.tool_window)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1500, in _tool_window_destroyed  
if tool_window in self._hide_tools_shown_states:  
AttributeError: 'MainWindow' object has no attribute
'_hide_tools_shown_states'  
  
AttributeError: 'MainWindow' object has no attribute
'_hide_tools_shown_states'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1500, in _tool_window_destroyed  
if tool_window in self._hide_tools_shown_states:  
  
See log for complete Python traceback.  
  

> toolshed show ISOLDE

> set selectionWidth 4

WARNING: no OpenCL or compatible CUDA drivers detected! While it is
theoretically possible to run ISOLDE using CPU only, in practice it is
prohibitively slow. If you have a suitable GPU in your machine, please check
that you have the recommended drivers from the manufacturer installed. The
current required CUDA version is 9.2 - if installed, please make sure this is
on your library path before starting ChimeraX.  

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1574, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/home/jinhui/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/__init__.py", line 48, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/tools.py", line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/home/jinhui/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/tool.py", line 168, in __init__  
self.isolde = isolde.Isolde(self)  
File "/home/jinhui/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 307, in __init__  
self._start_gui(gui)  
File "/home/jinhui/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 450, in _start_gui  
self._populate_menus_and_update_params()  
File "/home/jinhui/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 549, in
_populate_menus_and_update_params  
self._update_model_list(None, None, force=True)  
File "/home/jinhui/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 953, in _update_model_list  
from .restraints import MDFF_Mgr  
File "/home/jinhui/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/restraints/__init__.py", line 11, in <module>  
from ..molobject import Restraint_Change_Tracker  
File "/home/jinhui/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/molobject.py", line 41, in <module>  
_c_functions = CFunctions(os.path.splitext(libfile)[0])  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 23, in __init__  
self._c_lib = ctypes_open(library_path)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 261, in ctypes_open  
lib = ctypes.PyDLL(lib_path)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/ctypes/__init__.py", line
364, in __init__  
self._handle = _dlopen(self._name, mode)  
OSError: /home/jinhui/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1286, in <lambda>  
run(ses, "toolshed show %s" % StringArg.unparse(tool_name)))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 337, in toolshed_show  
bi.start_tool(session, tool_name)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 633, 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:  
/home/jinhui/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
/home/jinhui/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 633, 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.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 182, in <lambda>  
cb.clicked.connect(lambda e: self.cancel())  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 298, in cancel  
self.delete()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/tools.py", line 175, in delete  
self.session.ui.remove_tool(self)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 294, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 689, in remove_tool  
tw._destroy()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1716, in _destroy  
self.__toolkit.destroy()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1838, in destroy  
self.main_window._tool_window_destroyed(self.tool_window)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1500, in _tool_window_destroyed  
if tool_window in self._hide_tools_shown_states:  
AttributeError: 'MainWindow' object has no attribute
'_hide_tools_shown_states'  
  
AttributeError: 'MainWindow' object has no attribute
'_hide_tools_shown_states'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1500, in _tool_window_destroyed  
if tool_window in self._hide_tools_shown_states:  
  
See log for complete Python traceback.  
  

> show sel atoms

'ISOLDE_ToolUI' object has no attribute 'isolde'  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1811, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 552, in close_request  
tool_instance.delete()  
File "/home/jinhui/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/tool.py", line 180, in delete  
super().delete()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/tools.py", line 175, in delete  
self.session.ui.remove_tool(self)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 294, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 689, in remove_tool  
tw._destroy()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1716, in _destroy  
self.__toolkit.destroy()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1838, in destroy  
self.main_window._tool_window_destroyed(self.tool_window)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1500, in _tool_window_destroyed  
if tool_window in self._hide_tools_shown_states:  
AttributeError: 'MainWindow' object has no attribute
'_hide_tools_shown_states'  
  
AttributeError: 'MainWindow' object has no attribute
'_hide_tools_shown_states'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1500, in _tool_window_destroyed  
if tool_window in self._hide_tools_shown_states:  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 390.116
OpenGL renderer: GeForce GTX 960/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation