id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1874 ISOLDE: isolde/libmolc.so: undefined symbol mar2294@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-4.18.0-17-generic-x86_64-with-debian-buster-sid ChimeraX Version: 0.8 (2018-12-17) Description After installing ISOLDE 1.0b2 in ChimeraX 0.8, I attempted to launch it via the Tool menu. ISOLDE opens, but I get the error seein in the log contents. The ISOLDE window is open, but it doesn't recognize the PDB and .map files I have open, and I'm unable to get it to load the demo dataset (via the ""Load demo"" button) Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 0.8 (2018-12-17) How to cite UCSF ChimeraX > open /home/micah/Downloads/3j5q.pdb 3j5q.pdb title: Structure of TRPV1 ion channel In complex with DKTX and RTX determined by single particle electron cryo-microscopy [more info...] Chain information for 3j5q.pdb #1 --- Chain | Description A C F H | DKTX B D E G | transient receptor potential cation channel subfamily V member 1 > open /home/micah/Downloads/3j5q.pdb 3j5q.pdb title: Structure of TRPV1 ion channel In complex with DKTX and RTX determined by single particle electron cryo-microscopy [more info...] Chain information for 3j5q.pdb #2 --- Chain | Description A C F H | DKTX B D E G | transient receptor potential cation channel subfamily V member 1 > open /home/micah/Downloads/TRPV1_DkTx_RTX_sharpened_-150_3.8A.map Opened TRPV1_DkTx_RTX_sharpened_-150_3.8A.map, grid size 256,256,256, pixel 1.22, shown at level 2.92, step 1, values float32 > show selAtoms ribbons > hide selAtoms > toolshed show ISOLDE Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/toolshed/info.py"", line 579, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py"", line 1188, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) File ""/home/micah/.local/share/ChimeraX/0.8/site- packages/chimerax/isolde/__init__.py"", line 31, in start_tool return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/tools.py"", line 214, in get_singleton tinst = tool_class(session, tool_name, **kw) File ""/home/micah/.local/share/ChimeraX/0.8/site- packages/chimerax/isolde/tool.py"", line 159, in __init__ self.isolde = isolde.Isolde(self) File ""/home/micah/.local/share/ChimeraX/0.8/site- packages/chimerax/isolde/isolde.py"", line 315, in __init__ self._start_gui(gui) File ""/home/micah/.local/share/ChimeraX/0.8/site- packages/chimerax/isolde/isolde.py"", line 443, in _start_gui self._populate_menus_and_update_params() File ""/home/micah/.local/share/ChimeraX/0.8/site- packages/chimerax/isolde/isolde.py"", line 532, in _populate_menus_and_update_params self._update_model_list(None, None, force=True) File ""/home/micah/.local/share/ChimeraX/0.8/site- packages/chimerax/isolde/isolde.py"", line 919, in _update_model_list from .restraints import MDFF_Mgr File ""/home/micah/.local/share/ChimeraX/0.8/site- packages/chimerax/isolde/restraints/__init__.py"", line 11, in from ..molobject import Restraint_Change_Tracker File ""/home/micah/.local/share/ChimeraX/0.8/site- packages/chimerax/isolde/molobject.py"", line 42, in _c_functions = CFunctions(os.path.splitext(libfile)[0]) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/atomic/molc.py"", line 23, in __init__ self._c_lib = ctypes_open(library_path) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/atomic/molc.py"", line 261, in ctypes_open lib = ctypes.PyDLL(lib_path) File ""/usr/lib/ucsf-chimerax/lib/python3.6/ctypes/__init__.py"", line 348, in __init__ self._handle = _dlopen(self._name, mode) OSError: /home/micah/.local/share/ChimeraX/0.8/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/python3.6/site-packages/chimerax/ui/gui.py"", line 941, in run(ses, ""toolshed show %s"" % quote_if_necessary(tool_name))) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 2587, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/commands/toolshed.py"", line 337, in toolshed_show bi.start_tool(session, tool_name) File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/toolshed/info.py"", line 585, 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/micah/.local/share/ChimeraX/0.8/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/micah/.local/share/ChimeraX/0.8/site- packages/chimerax/isolde/libmolc.so: undefined symbol: _ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE File ""/usr/lib/ucsf-chimerax/lib/python3.6/site- packages/chimerax/core/toolshed/info.py"", line 585, 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 410.104 OpenGL renderer: GeForce GTX 1070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Third Party wontfix Tom Goddard all ChimeraX