id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2247 Residue::find_atom missing from _ISOLDES_ libmolc.so?!? chimerax-bug-report@… Conrad Huang "{{{ The following bug report has been submitted: Platform: Linux-4.15.0-54-generic-x86_64-with-debian-buster-sid ChimeraX Version: 0.91 (2019-07-03) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.91 (2019-07-03) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open cis22a.mol2 Opened cis22a.mol2 containing 1 structures (54 atoms, 57 bonds) > toolshed show ""Basic Actions"" > toolshed show Toolbar > 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 1511, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) File ""/home/micael/.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/micael/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/tool.py"", line 168, in __init__ self.isolde = isolde.Isolde(self) File ""/home/micael/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 307, in __init__ self._start_gui(gui) File ""/home/micael/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 444, in _start_gui self._populate_menus_and_update_params() File ""/home/micael/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 543, in _populate_menus_and_update_params self._update_model_list(None, None, force=True) File ""/home/micael/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 947, in _update_model_list from .restraints import MDFF_Mgr File ""/home/micael/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/restraints/__init__.py"", line 11, in from ..molobject import Restraint_Change_Tracker File ""/home/micael/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/molobject.py"", line 41, in _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 356, in __init__ self._handle = _dlopen(self._name, mode) OSError: /home/micael/.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 1135, in run(ses, ""toolshed show %s"" % quote_if_necessary(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 2646, 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/micael/.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/micael/.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. 'ISOLDE_ToolUI' object has no attribute 'isolde' > 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 1511, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) File ""/home/micael/.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/micael/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/tool.py"", line 168, in __init__ self.isolde = isolde.Isolde(self) File ""/home/micael/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 307, in __init__ self._start_gui(gui) File ""/home/micael/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 444, in _start_gui self._populate_menus_and_update_params() File ""/home/micael/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 543, in _populate_menus_and_update_params self._update_model_list(None, None, force=True) File ""/home/micael/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 947, in _update_model_list from .restraints import MDFF_Mgr File ""/home/micael/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/restraints/__init__.py"", line 11, in from ..molobject import Restraint_Change_Tracker File ""/home/micael/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/molobject.py"", line 41, in _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 356, in __init__ self._handle = _dlopen(self._name, mode) OSError: /home/micael/.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 1135, in run(ses, ""toolshed show %s"" % quote_if_necessary(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 2646, 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/micael/.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/micael/.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. OpenGL version: 3.3.0 NVIDIA 390.116 OpenGL renderer: GeForce GTX 1060/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Tool Shed duplicate Tristan Croll all ChimeraX