Using wrong Linux distro?

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.3.0-42-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.91 (2019-12-23)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.91 (2019-12-23)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/mpillana/AD41_MARZO_2020/vi_vii/bla.cxs

opened ChimeraX session  

> help help:user

> hide #10.9 models

> show #10.9 models

> select #10.9

83 atoms, 85 bonds, 1 model selected  

> select #9

2 models selected  

> select #10.9

83 atoms, 85 bonds, 1 model selected  

> toolshed show "Fit to Segments"

Density map not found or not selected  

> select #9

2 models selected  
Density map not found or not selected  
Density map not found or not selected  
Density map not found or not selected  
Density map not found or not selected  

> select clear

> select #9

2 models selected  

> ~select #9

Nothing selected  

> select #9

2 models selected  
Density map not found or not selected  
Density map not found or not selected  
Density map not found or not selected  
Density map not found or not selected  
Density map not found or not selected  
Density map not found or not selected  
Density map not found or not selected  

> select clear

Density map not found or not selected  

> volume #9 level 0.01862

> volume #9 level 0.007911

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 1843, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 580, in close_request  
tool_instance.delete()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 496, in delete  
ToolInstance.delete(self)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 176, in delete  
self.session.tools.remove([self])  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 360, in remove  
del self._tool_instances[tid]  
KeyError: 8  
  
KeyError: 8  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 360, in remove  
del self._tool_instances[tid]  
  
See log for complete Python traceback.  
  
Downloading bundle ChimeraX_ISOLDE-1.0b4-cp37-cp37m-linux_x86_64.whl  
Successfully installed ChimeraX-ISOLDE-1.0b4  
Installed ChimeraX-ISOLDE (1.0b4)  

> toolshed show "Model Panel"

> show #!8 models

> toolshed show ISOLDE

> set selectionWidth 4

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/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/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 "/home/mpillana/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/__init__.py", line 128, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/home/mpillana/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/tool.py", line 168, in __init__  
self.isolde = isolde.Isolde(self)  
File "/home/mpillana/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 312, in __init__  
self._start_gui(gui)  
File "/home/mpillana/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 456, in _start_gui  
self._populate_menus_and_update_params()  
File "/home/mpillana/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 557, in
_populate_menus_and_update_params  
self._update_model_list(None, None, force=True)  
File "/home/mpillana/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 967, in _update_model_list  
from .restraints import MDFFMgr  
File "/home/mpillana/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/restraints/__init__.py", line 11, in <module>  
from ..molobject import RestraintChangeTracker  
File "/home/mpillana/.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/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/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 261, in ctypes_open  
lib = ctypes.PyDLL(lib_path)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/ctypes/__init__.py", line 364, in
__init__  
self._handle = _dlopen(self._name, mode)  
OSError: /home/mpillana/.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/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 1315, in <lambda>  
run(ses, "toolshed show %s" % StringArg.unparse(tool_name)))  
File "/usr/lib/ucsf-chimerax/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/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/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 339, in toolshed_show  
bi.start_tool(session, name)  
File "/usr/lib/ucsf-chimerax/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/mpillana/.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/mpillana/.local/share/ChimeraX/0.91/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE  
  
File "/usr/lib/ucsf-chimerax/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.  
  




OpenGL version: 3.3.0 NVIDIA 440.64
OpenGL renderer: GeForce MX130/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tristan Croll]

Yep - duplicate of #2214. Should go away once people update to 0.93 and later.