id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1494 Cage Builder: name 'place_model' is not defined Scooter Morris Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-18.2.0-x86_64-i386-64bit ChimeraX Version: 0.8 (2018-11-11) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.8 (2018-11-11) How to cite UCSF ChimeraX > open 3w7f format mmCIF fromDatabase pdb 3w7f title: Crystal structure of the C(30) carotenoid dehydrosqualene synthase from staphylococcus aureus complexed with farnesyl thiopyrophosphate [more info...] Chain information for 3w7f #1 --- Chain | Description A B | Dehydrosqualene synthase 3w7f mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > view > view sel > toolshed show ""Side View"" > view > toolshed show ""Side View"" > view sel > view Unknown command: usae > usage Use 'usage ' for a command synopsis. Use 'help ' to learn more about a command. Exception ignored in: > Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/opengl.py"", line 1739, in __del__ % self.name) RuntimeError: OpenGL framebuffer mask was not deleted before core.graphics.Framebuffer destroyed Exception ignored in: > Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/opengl.py"", line 2505, in __del__ raise RuntimeError('OpenGL texture was not deleted before core.graphics.Texture destroyed') RuntimeError: OpenGL texture was not deleted before core.graphics.Texture destroyed Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/info.py"", line 272, in _register_cmd api._api_caller.register_command(api, self, ci, logger) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py"", line 1189, in register_command return cls._get_func(api, ""register_command"")(ci.name, logger) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/cage_builder/__init__.py"", line 28, in register_command cmd.register_cage_command(logger) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/cage_builder/cmd.py"", line 84, in register_cage_command required_arguments = [place_model], NameError: name 'place_model' is not defined During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 1886, in lazy_register deferred.call() File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 1816, in call return self.proxy() File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/info.py"", line 265, in cb s._register_cmd(ci, l) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/info.py"", line 275, 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 cage in bundle ChimeraX-Cage-Builder: name 'place_model' is not defined During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/cmd_line/tool.py"", line 220, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 2581, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/std_commands/usage.py"", line 31, in usage cmds = cli.registered_commands(multiword=True) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 2997, in registered_commands return list(cmds('', parent_info)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 2980, in cmds word_info.lazy_register(word) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 1888, in lazy_register raise RuntimeError(""delayed command registration for %r failed (%s)"" % (cmd_name, e)) RuntimeError: delayed command registration for 'cage' failed (register_command() failed for command cage in bundle ChimeraX-Cage-Builder: name 'place_model' is not defined) RuntimeError: delayed command registration for 'cage' failed (register_command() failed for command cage in bundle ChimeraX-Cage-Builder: name 'place_model' is not defined) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 1888, in lazy_register raise RuntimeError(""delayed command registration for %r failed (%s)"" % (cmd_name, e)) See log for complete Python traceback. OpenGL version: 4.1 ATI-2.2.8 OpenGL renderer: AMD Radeon Pro 555X OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect closed normal Higher-Order Structure duplicate all ChimeraX