id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1943 Error using named selection holding deleted model Elaine Meng Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-18.5.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-05-15) Description TypeError: object of type 'NoneType' has no len() User-defined selection in Select menu ""blob"" (selected volume isosurface) did not go away when volume model was closed. Choosing it from menu after closing the volume model caused the traceback shown in the Log. Can create volume isosurf to test with molmap, e.g. open 2gbp molmap ligand 8 (Ctrl-click isosurf to select it) name frozen blob sel close (choose ""blob"" from menu) Log: UCSF ChimeraX version: 0.9 (2019-05-15) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > help help:credits.html > open 2gbp format mmCIF fromDatabase pdb 2gbp title: Sugar and signal-transducer binding sites of the escherichia coli galactose chemoreceptor protein [more info...] Chain information for 2gbp #1 --- Chain | Description A | D-galactose/D-glucose binding protein Non-standard residues in 2gbp #1 --- BGC — β-D-glucose CA — calcium ion > molmap ligand 8 > select #2 2 models selected > view sel > view cofr false > name trips :trp > name frozen blob sel > select clear > select blob 2 models selected > select trips 70 atoms, 75 bonds selected > show selAtoms > open 1zik 1zik title: GCN4-leucine zipper core mutant ASN16LYS In the dimeric state [more info...] Chain information for 1zik #3 --- Chain | Description A B | general control protein GCN4 > sequence chain /b Alignment identifier is 3.B Unknown command: sequence dissoc :1 Unknown command: sequence dissoc :1 Unknown command: sequence dissoc 1 Unknown command: sequence dissoc 1 Unknown command: sequence dissoc 1 Unknown command: sequence dissoc 1 > close > open 1zik 1zik title: GCN4-leucine zipper core mutant ASN16LYS In the dimeric state [more info...] Chain information for 1zik #1 --- Chain | Description A B | general control protein GCN4 > sequence chain /b Alignment identifier is 1.B > sequence associate /a 1 Associated 1zik chain A to chain B with 0 mismatches Unknown command: sequence dissoc /a Unknown command: sequence dissoc /a Unknown command: sequence dissoc /a Unknown command: sequence dissoc /a Unknown command: sequence dissoc /b Unknown command: sequence dissoc /b Unknown command: sequence dissoc /a 1.B Unknown command: sequence dissoc /a 1.B > close session > open 1zik 1zik title: GCN4-leucine zipper core mutant ASN16LYS In the dimeric state [more info...] Chain information for 1zik #1 --- Chain | Description A B | general control protein GCN4 > sequence chain /b Alignment identifier is 1.B > sequence associate /a Associated 1zik chain A to chain B with 0 mismatches Unknown command: sequence dissoc /a Unknown command: sequence dissoc /a Unknown command: sequence dissoc /a 1.B Unknown command: sequence dissoc /a 1.B > sequence associate /a :1 Disassociated 1zik chain A from chain B Associated 1zik chain A to chain B with 0 mismatches > sequence associate /a :2 Disassociated 1zik chain A from chain B Associated 1zik chain A to chain B with 0 mismatches > sequence associate /a 1 Disassociated 1zik chain A from chain B Associated 1zik chain A to chain B with 0 mismatches > sequence associate /a ""chain B"" Disassociated 1zik chain A from chain B Associated 1zik chain A to chain B with 0 mismatches > select blob Traceback (most recent call last): File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 1017, in selectors_menu.triggered.connect(lambda name, ses=self.session, run=run: run(ses, ""sel "" + name.text())) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2631, in run result = ci.function(session, **kw_args) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/std_commands/select.py"", line 48, in select modify_selection(objects, 'add', undo_state, full_residues = residues) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/std_commands/select.py"", line 207, in modify_selection m.selected = select File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 234, in __setattr__ super(Drawing, self).__setattr__(key, value) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 1048, in _set_selected Model.set_selected(self, sel, fire_trigger=fire_trigger) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 172, in set_selected Drawing.set_highlighted(self, sel) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 375, in set_highlighted self._highlighted_positions = ones(len(self.positions), bool) TypeError: object of type 'NoneType' has no len() TypeError: object of type 'NoneType' has no len() File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 375, in set_highlighted self._highlighted_positions = ones(len(self.positions), bool) See log for complete Python traceback. > select trips Nothing selected OpenGL version: 4.1 INTEL-12.8.38 OpenGL renderer: Intel Iris Pro OpenGL Engine OpenGL vendor: Intel Inc. }}} " defect closed normal Core fixed Eric Pettersen all ChimeraX