id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2425 ISOLDE cannot find symbol atomstruct::Residue::find_atom 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 (2019-09-18) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.91 (2019-09-18) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /media/yanyan/cpn_ATP_072818/102818/Class3D/job171/run_it025_class001_zflip.mrc Opened run_it025_class001_zflip.mrc, grid size 280,280,280, pixel 1.08, shown at level 0.00466, step 2, values float32 > open /media/yanyan/cpn_ATP_072818/102818/model/double_subunit_class1_on_class1.pdb Summary of feedback from opening /media/yanyan/cpn_ATP_072818/102818/model/double_subunit_class1_on_class1.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 3866 messages similar to the above omitted Chain information for double_subunit_class1_on_class1.pdb #2 --- Chain | Description A | No description available B | No description available > toolshed show ISOLDE > set selectionWidth 4 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/yanyan/.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/yanyan/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/tool.py"", line 168, in __init__ self.isolde = isolde.Isolde(self) File ""/home/yanyan/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 307, in __init__ self._start_gui(gui) File ""/home/yanyan/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 450, in _start_gui self._populate_menus_and_update_params() File ""/home/yanyan/.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/yanyan/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 953, in _update_model_list from .restraints import MDFF_Mgr File ""/home/yanyan/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/restraints/__init__.py"", line 11, in from ..molobject import Restraint_Change_Tracker File ""/home/yanyan/.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 364, in __init__ self._handle = _dlopen(self._name, mode) OSError: /home/yanyan/.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 1275, 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 2737, 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/yanyan/.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/yanyan/.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 430.26 OpenGL renderer: GeForce GTX 1080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Tool Shed fixed Greg Couch Tristan Croll all ChimeraX