id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4206 Can't select atom with empty chain id goddard@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.2.dev202101290243 (2021-01-29 02:43:44 UTC) Description Ctrl-click to select an atom produces an invalid select command if the chain identifier is the empty string. Also it produces an error if the serial number has not been set. I was looking at a molecule made from a Gaussian cube file (small molecule) using a Python script. I attach an mmCIF version that has serial numbers but no chain id. Log: UCSF ChimeraX version: 1.2.dev202101290243 (2021-01-29) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/goddard/Downloads/wfc_K001_B329wfc.cube Opened wfc_K001_B329wfc.cube as #1, grid size 360,360,360, pixel 0.0321, shown at level -0.00109,0.00109, step 2, values float32 > open > /Users/goddard/ucsf/chimerax/src/bundles/map_data/src/gaussian/make_atoms.py Created 1 atomic models for 1 Gaussian Cube files executed make_atoms.py > select /:1@@serial_number=-1 Expected an objects specifier or a keyword > select /:1@@serial_number=-1 Expected an objects specifier or a keyword > select /:1@@serial_number=-1 Expected an objects specifier or a keyword > close #2 > open > /Users/goddard/ucsf/chimerax/src/bundles/map_data/src/gaussian/make_atoms.py Created 1 atomic models for 1 Gaussian Cube files executed make_atoms.py Drag select of 2 atoms > select /:1@@serial_number=90 Expected an objects specifier or a keyword > select /A:1@@serial_number=90 Nothing selected Drag select of 20 atoms > save /Users/goddard/Desktop/test.mmcif models #2 > open /Users/goddard/Desktop/test.mmcif format mmcif Summary of feedback from opening /Users/goddard/Desktop/test.mmcif --- warnings | Unable to infer polymer connectivity due to unspecified label_seq_id for residue ""UNK"" near line 90 Atom Al is not in the residue template for UNK /:1 > hide #2 models > select #3/:1@@serial_number=58 Expected an objects specifier or a keyword OpenGL version: 4.1 ATI-3.10.18 OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,3 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 32 GB Boot ROM Version: 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0) Software: System Software Overview: System Version: macOS 10.15.7 (19H2) Kernel Version: Darwin 19.6.0 Time since boot: 49 days 10:42 Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal: Supported, feature set macOS GPUFamily2 v1 Radeon Pro Vega 20: Chipset Model: Radeon Pro Vega 20 Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x69af Revision ID: 0x00c0 ROM Revision: 113-D2060I-087 VBIOS Version: 113-D20601MA0T-016 Option ROM Version: 113-D20601MA0T-016 EFI Driver Version: 01.01.087 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2880 x 1800 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Locale: ('en_US', 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.0 backcall: 0.2.0 biopython: 1.78 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.3.1 chardet: 3.0.4 ChimeraX-AddCharge: 1.0 ChimeraX-AddH: 2.1.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.11 ChimeraX-AtomicLibrary: 1.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.4 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 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sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.2.0 File attachment: test.mmcif }}} [attachment:""test.mmcif""] " defect closed minor Command Line fixed all ChimeraX