ISOLDE cannot link Residue::find_atom

[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  

> 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