id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3180 Save options widgets deleted ubaumann@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-19.4.0-x86_64-i386-64bit ChimeraX Version: 1.0 (2020-05-08) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.0rc202005080235 (2020-05-08) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 3rvz Summary of feedback from opening 3rvz fetched from pdb --- notes | Fetching compressed mmCIF 3rvz from http://files.rcsb.org/download/3rvz.cif Fetching CCD PX4 from http://ligand-expo.rcsb.org/reports/P/PX4/PX4.cif 3rvz title: Crystal structure of the NavAb voltage-gated sodium channel (Ile217Cys, 2.8 A) [more info...] Chain information for 3rvz #1 --- Chain | Description A B | Ion transport protein Non-standard residues in 3rvz #1 --- PX4 — 1,2-dimyristoyl-Sn-glycero-3-phosphocholine 3rvz mmCIF Assemblies --- 1| author_and_software_defined_assembly > sym #1 assembly 1 > view > color #2 bychain > hide atoms > cartoon style modeHelix tube r2. Expected a keyword > cartoon style modeHelix tube radius 2. > rainbow #2 > show :arg atoms > color #2 byhetero > style #2 ball Changed 3728 atom styles > cartoon style modeHelix tube radius 1.5 > save /Users/ubaumann/Desktop/image1.png supersample 3 > save /Users/ubaumann/Documents/Vorlesungen/MN-BC- > BC1.2/SS2020/PIccies/sodium-channel-3rvz.cxs > close session > open 3lut Summary of feedback from opening 3lut fetched from pdb --- note | Fetching compressed mmCIF 3lut from http://files.rcsb.org/download/3lut.cif 3lut title: A Structural Model for the Full-length Shaker Potassium Channel Kv1.2 [more info...] Chain information for 3lut #1 --- Chain | Description A | Voltage-gated potassium channel subunit beta-2 B | Potassium voltage-gated channel subfamily A member 2 Non-standard residues in 3lut #1 --- K — potassium ion NAP — nadp nicotinamide-adenine-dinucleotide phosphate (2'-monophosphoadenosine 5'-diphosphoribose) 3lut mmCIF Assemblies --- 1| author_and_software_defined_assembly > close session > open 1k4c 1k4c title: Potassium Channel KcsA-Fab complex in high concentration of K+ [more info...] Chain information for 1k4c #1 --- Chain | Description A | antibody Fab fragment heavy chain B | antibody Fab fragment light chain C | potassium channel KcsA Non-standard residues in 1k4c #1 --- DGA — diacyl glycerol F09 — nonan-1-ol K — potassium ion 1k4c mmCIF Assemblies --- 1| author_defined_assembly > sym #1 assembly 1 > view > close session > open 31ut Fetching url http://files.rcsb.org/download/31ut.cif failed: HTTP Error 404: Not Found > open 3lut format mmcif fromDatabase pdb 3lut title: A Structural Model for the Full-length Shaker Potassium Channel Kv1.2 [more info...] Chain information for 3lut #1 --- Chain | Description A | Voltage-gated potassium channel subunit beta-2 B | Potassium voltage-gated channel subfamily A member 2 Non-standard residues in 3lut #1 --- K — potassium ion NAP — nadp nicotinamide-adenine-dinucleotide phosphate (2'-monophosphoadenosine 5'-diphosphoribose) 3lut mmCIF Assemblies --- 1| author_and_software_defined_assembly > close session > open 31utopen 2a79 '31utopen' has no suffix > open 2a79 Summary of feedback from opening 2a79 fetched from pdb --- note | Fetching compressed mmCIF 2a79 from http://files.rcsb.org/download/2a79.cif 2a79 title: Mammalian Shaker Kv1.2 potassium channel- β subunit complex [more info...] Chain information for 2a79 #1 --- Chain | Description A | Voltage-gated potassium channel beta-2 subunit B | Potassium voltage-gated channel subfamily A member 2 C | poly-unknown chain D | poly-unknown chain Non-standard residues in 2a79 #1 --- K — potassium ion NAP — nadp nicotinamide-adenine-dinucleotide phosphate (2'-monophosphoadenosine 5'-diphosphoribose) 2a79 mmCIF Assemblies --- 1| author_defined_assembly > sym #1 assembly 1 > view > delete /B > close session > open 2a79 format mmcif fromDatabase pdb 2a79 title: Mammalian Shaker Kv1.2 potassium channel- β subunit complex [more info...] Chain information for 2a79 #1 --- Chain | Description A | Voltage-gated potassium channel beta-2 subunit B | Potassium voltage-gated channel subfamily A member 2 C | poly-unknown chain D | poly-unknown chain Non-standard residues in 2a79 #1 --- K — potassium ion NAP — nadp nicotinamide-adenine-dinucleotide phosphate (2'-monophosphoadenosine 5'-diphosphoribose) 2a79 mmCIF Assemblies --- 1| author_defined_assembly > sym #1 assembly 1 > view > delete /A > cartoon style modeHelix tube radius 1.5 > rainbow #!2 > hide atoms > show :K atoms Traceback (most recent call last): File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/toolbar/tool.py"", line 162, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 453, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py"", line 1660, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/toolbar/__init__.py"", line 38, in run_provider providers.run_provider(session, name) File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/toolbar/providers.py"", line 45, in run_provider what(session) File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/toolbar/providers.py"", line 27, in _file_save show_save_file_dialog(session) File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 122, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 24, in display self._customize_dialog(session, dialog) File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 86, in _customize_dialog self._format_selected(session, dialog) File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 98, in _format_selected self._options_layout.addWidget(self._current_option) RuntimeError: wrapped C/C++ object of type SaveOptionsWidget has been deleted RuntimeError: wrapped C/C++ object of type SaveOptionsWidget has been deleted File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 98, in _format_selected self._options_layout.addWidget(self._current_option) See log for complete Python traceback. OpenGL version: 4.1 NVIDIA-14.0.32 355.11.11.10.10.143 OpenGL renderer: NVIDIA GeForce GTX 775M OpenGL Engine OpenGL vendor: NVIDIA CorporationHardware: Hardware Overview: Model Name: iMac Model Identifier: iMac14,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 3.4 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Memory: 16 GB Boot ROM Version: 142.0.0.0.0 SMC Version (system): 2.15f7 Software: System Software Overview: System Version: macOS 10.15.4 (19E287) Kernel Version: Darwin 19.4.0 Time since boot: 10:56 Graphics/Displays: NVIDIA GeForce GTX 775M: Chipset Model: NVIDIA GeForce GTX 775M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 2 GB Vendor: NVIDIA (0x10de) Device ID: 0x119d Revision ID: 0x00a2 ROM Revision: 3782 Metal: Supported, feature set macOS GPUFamily1 v4 Displays: iMac: Display Type: LCD Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal }}} " defect closed normal Input/Output duplicate all ChimeraX