id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2161 Residue::find_atom missing from _ISOLDES_ libmolc.so?!? Eric Pettersen Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-4.15.0-54-generic-x86_64-with-debian-buster-sid ChimeraX Version: 0.91 (2019-07-02) Description Running 'isolde tutorial' after installing ISOLDE for the first time for that account Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 0.91 (2019-07-02) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > isolde tutorial isolde is provided by the uninstalled bundle ISOLDE Downloading bundle ChimeraX_ISOLDE-1.0b3.dev1-cp37-cp37m-linux_x86_64.whl Successfully installed ChimeraX-Clipper-0.9.6 ChimeraX-ISOLDE-1.0b3.dev1 Installed ChimeraX-Clipper (0.9.6) Installed ChimeraX-ISOLDE (1.0b3.dev1) 'clip' is a prefix of an existing command 'clipper' Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 297, in _register_cmd api._api_caller.register_command(api, self, ci, logger) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py"", line 1515, in register_command return cls._get_func(api, ""register_command"")(ci.name, logger) File ""/home/chimera/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/__init__.py"", line 57, in register_command cmd.register_isolde(logger) File ""/home/chimera/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/cmd.py"", line 144, in register_isolde from chimerax.isolde.restraints.cmd import register_isolde_restrain File ""/home/chimera/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/restraints/__init__.py"", line 11, in from ..molobject import Restraint_Change_Tracker File ""/home/chimera/.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/chimera/.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/core/commands/cli.py"", line 1935, in lazy_register deferred.call() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 1866, in call return self.proxy() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 287, in cb s._register_cmd(ci, l) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 300, in _register_cmd ""register_command() failed for command %s in bundle %s:\n%s"" % (ci.name, self.name, str(e))) chimerax.core.toolshed.ToolshedError: register_command() failed for command isolde in bundle ChimeraX-ISOLDE: /home/chimera/.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/cmd_line/tool.py"", line 254, in execute cmd.run(cmd_text) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2587, in run self._find_command_name(final, used_aliases=_used_aliases) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2330, in _find_command_name what.lazy_register(cmd_name) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 1937, in lazy_register raise RuntimeError(""delayed command registration for %r failed (%s)"" % (cmd_name, e)) RuntimeError: delayed command registration for 'isolde' failed (register_command() failed for command isolde in bundle ChimeraX-ISOLDE: /home/chimera/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/libmolc.so: undefined symbol: _ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE) RuntimeError: delayed command registration for 'isolde' failed (register_command() failed for command isolde in bundle ChimeraX-ISOLDE: /home/chimera/.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/commands/cli.py"", line 1937, in lazy_register raise RuntimeError(""delayed command registration for %r failed (%s)"" % (cmd_name, e)) See log for complete Python traceback. OpenGL version: 4.5 (Core Profile) Mesa 18.2.8 OpenGL renderer: AMD TAHITI (DRM 2.50.0, 4.15.0-54-generic, LLVM 7.0.0) OpenGL vendor: X.Org }}} " defect closed normal Third Party duplicate Conrad Huang 2160 all ChimeraX