id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5137 Toolbar appearance changed on Mac goddard@… Zach Pearson "{{{ The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.3.dev202108251821 (2021-08-25 18:21:58 UTC) Description A change to the Toolbar formatting has made the spacing between category names and the icons even greater than before -- ie even uglier. Commit was August 30 by Zach. The new appearance uses less vertical space for the tabs which is good, but overall appearance is worse. Log: UCSF ChimeraX version: 1.3.dev202108251821 (2021-08-25) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 5r43 Summary of feedback from opening 5r43 fetched from pdb --- notes | Fetching compressed mmCIF 5r43 from http://files.rcsb.org/download/5r43.cif Fetching CCD MLA from http://ligand-expo.rcsb.org/reports/M/MLA/MLA.cif Fetching CCD IOD from http://ligand-expo.rcsb.org/reports/I/IOD/IOD.cif 5r43 title: Crystal Structure of deuterated gamma-Chymotrypsin at pH 7.5, cryo temperature [more info...] Chain information for 5r43 #1 --- Chain | Description | UniProt A | Chymotrypsinogen A | CTRA_BOVIN B | Chymotrypsinogen A | CTRA_BOVIN C | Chymotrypsinogen A | CTRA_BOVIN D | peptide SWPW | E | peptide TPGVY | Non-standard residues in 5r43 #1 --- IOD — iodide ion MLA — malonic acid (dicarboxylic acid C3; propanediolic acid; methanedicarboxylic acid) > show cartoons > hide atoms > ui tool show AlphaFold > alphafold match #1/A 1 UniProt id does not have an AlphaFold database model: P00766 (chain A) No AlphaFold model with similar sequence for chain A Opened 0 AlphaFold model > alphafold search #1/A ChimeraX REST job id: job_nwl1j4lr BlastProtein finished. Parsing BLAST results. > select /A:1-10 68 atoms, 69 bonds, 10 residues, 1 model selected > select /B:16-146 980 atoms, 1001 bonds, 131 residues, 1 model selected > alphafold match #1/B 1 UniProt id does not have an AlphaFold database model: P00766 (chain B) Fetching compressed AlphaFold P17538 from https://alphafold.ebi.ac.uk/files/AF-P17538-F1-model_v1.cif 1 AlphaFold model found using sequence similarity searches: P17538 (chain B) AlphaFold chains matching 5r43 --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id B | CTRB1_HUMAN | P17538 | 0.53 | 131 | 131 | 83 Opened 1 AlphaFold model > color #2 lightgray > color #2::same_sequence=false red > hide #1 models > show #1 models > alphafold match #1/C 1 UniProt id does not have an AlphaFold database model: P00766 (chain C) 1 AlphaFold model found using sequence similarity searches: P17538 (chain C) AlphaFold chains matching 5r43 --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id C | CTRB1_HUMAN | P17538 | 0.62 | 98 | 97 | 81 Opened 1 AlphaFold model > alphafold search #1/C ChimeraX REST job id: job_560pdysu BlastProtein finished. Parsing BLAST results. > alphafold fetch Q561U4 alignTo #1/C Fetching compressed AlphaFold Q561U4 from https://alphafold.ebi.ac.uk/files/AF-Q561U4-F1-model_v1.cif AlphaFold chains matching chain C --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id C | | Q561U4 | 0.65 | 97 | 97 | 68 > hide #1 models > close #2 > hide #4 models > show #4 models > hide #4 models > show #4 models > alphafold fetch G3V8J3 alignTo #1/C Fetching compressed AlphaFold G3V8J3 from https://alphafold.ebi.ac.uk/files/AF-G3V8J3-F1-model_v1.cif AlphaFold chains matching chain C --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id C | | G3V8J3 | 0.74 | 98 | 97 | 54 > open 7p4z format mmcif fromDatabase pdb 7p4z title: Crystal structure of avidin from hen egg white in space group C2 [more info...] Chain information for 7p4z #5 --- Chain | Description | UniProt A B | Avidin | AVID_CHICK Non-standard residues in 7p4z #5 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) 7p4z mmCIF Assemblies --- 1| author_and_software_defined_assembly > close #1-4 > alphafold match #1/C No protein sequences specified > alphafold match #5/A 1 UniProt id does not have an AlphaFold database model: P02701 (chain A) No AlphaFold model with similar sequence for chain A Opened 0 AlphaFold model > alphafold search #5/A ChimeraX REST job id: job_fp52nm5o BlastProtein finished. Parsing BLAST results. > alphafold fetch A0A2R8PXI9 alignTo #5/A AlphaFold chains matching chain A --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id A | | A0A2R8PXI9 | 1.90 | 122 | 116 | 40 > alphafold predict #5/A Running AlphaFold prediction AlphaFold prediction finished Results in /Users/goddard/Downloads/ChimeraX/AlphaFold/prediction_9 Chain information for best_model.pdb #2 --- Chain | Description A | No description available OpenGL version: 4.1 ATI-3.10.19 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: 1554.100.64.0.0 (iBridge: 18.16.14556.0.0,0) Software: System Software Overview: System Version: macOS 10.15.7 (19H1030) Kernel Version: Darwin 19.6.0 Time since boot: 103 days 1:11 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: (None, '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: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.0 chardet: 4.0.0 charset-normalizer: 2.0.4 ChimeraX-AddCharge: 1.1.4 ChimeraX-AddH: 2.1.10 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.28.1 ChimeraX-AtomicLibrary: 4.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.3 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-ColorKey: 1.3.3 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3.dev202108251821 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.4 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0 ChimeraX-MDcrds: 2.4 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.1 ChimeraX-ModelPanel: 1.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.5.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.1 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.12 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 comtypes: 1.1.10 cxservices: 1.0.1 cycler: 0.10.0 Cython: 0.29.23 decorator: 5.0.9 distlib: 0.3.1 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.3.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.20 imagecodecs: 2021.4.28 imagesize: 1.2.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 2.11.3 jupyter-client: 6.1.12 jupyter-core: 4.7.1 kiwisolver: 1.3.1 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 1.1.1 matplotlib: 3.4.2 matplotlib-inline: 0.1.2 msgpack: 1.0.2 netCDF4: 1.5.6 networkx: 2.6.2 numexpr: 2.7.3 numpy: 1.21.0 numpydoc: 1.1.0 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.2 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.2.0 pip: 21.1.1 pkginfo: 1.7.0 prompt-toolkit: 3.0.19 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.9.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.2.1 qtconsole: 5.1.0 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.25.1 scipy: 1.6.3 setuptools: 57.0.0 sfftk-rw: 0.7.0.post1 six: 1.16.0 snowballstemmer: 2.1.0 sortedcontainers: 2.4.0 Sphinx: 4.0.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.26.6 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.2 wheel-filename: 1.3.0 }}} " defect closed blocker 1.3 UI fixed Greg Couch Eric Pettersen Elaine Meng all ChimeraX