id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6180 Tug mouse mode run away goddard@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-12.0.1-x86_64-i386-64bit ChimeraX Version: 1.4.dev202202151837 (2022-02-15 18:37:03 UTC) Description Tugging with mouse on a model that is rotated relative to scene coordinates tugs in the wrong direction and runs away. Apparently a scene coordinate versus model coordinate problem. Log: UCSF ChimeraX version: 1.4.dev202202151837 (2022-02-15) © 2016-2021 Regents of the University of California. All rights reserved. > open /Users/goddard/ucsf/presentations/vr-nih-feb2022/data/ferritin.cxs > format session Opened emdb 12873 as #4, grid size 480,480,480, pixel 0.652, shown at level 0.00424, step 2, values float32 Opened emdb 12873 gaussian as #6, grid size 120,120,120, pixel 2.61, shown at level 0.0039, step 1, values float32 Log from Tue Feb 15 17:17:52 2022 Startup Messages --- warning | Data format provider 'ZDOCK' supplied unknown keywords with format description: {'is_default': 'false'} UCSF ChimeraX version: 1.4.dev202202151837 (2022-02-15) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 5n5f 5n5f title: Crystal structure of Haliangium ochraceum encapsulated ferritin [more info...] Chain information for 5n5f #1 --- Chain | Description | UniProt A B C D E F G H I J | encapsulated ferritin | D0LZ73_HALO1 Non-standard residues in 5n5f #1 --- NA — sodium ion > open /Users/goddard/Downloads/ChimeraX/AlphaFold/prediction_1/best_model.pdb > format pdb Chain information for best_model.pdb #2 --- Chain | Description A | No description available > mmaker #2 to #1/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 5n5f, chain A (#1) with best_model.pdb, chain A (#2), sequence alignment score = 489.2 RMSD between 91 pruned atom pairs is 0.463 angstroms; (across all 91 pairs: 0.463) > show atoms > ui mousemode right tug > open 12873 fromDatabase emdb Summary of feedback from opening 12873 fetched from emdb --- note | Fetching compressed map 12873 from ftp://ftp.wwpdb.org/pub/emdb/structures/EMD-12873/map/emd_12873.map.gz Opened emdb 12873 as #4, grid size 480,480,480, pixel 0.652, shown at level 0.0165, step 2, values float32 > view > open 7oe2 format mmcif fromDatabase pdb 7oe2 title: Model of closed pentamer of the Haliangium ochraceum encapsulin from symmetry expansion of icosahedral single particle reconstruction [more info...] Chain information for 7oe2 #5 --- Chain | Description | UniProt 1 2 3 4 5 | Haliangium ochraceum Encapsulated ferritin localisation sequence | D0LZ73_HALO1 A B C D E | Linocin_M18 bacteriocin protein | D0LZ74_HALO1 > volume #4 level 0.00424 > hide #2 models > hide #!1 models > fitmap #5 inMap #4 Fit molecule 7oe2 (#5) to map emdb 12873 (#4) using 10589 atoms average map value = 0.004732, steps = 292 shifted from previous position = 24.9 rotated from previous position = 24.5 degrees atoms outside contour = 5952, contour level = 0.0042398 Position of 7oe2 (#5) relative to emdb 12873 (#4) coordinates: Matrix rotation and translation 0.91053976 -0.19232066 -0.36596462 89.05634354 0.17864635 0.98133200 -0.07122497 -46.71185116 0.37283082 -0.00052507 0.92789919 -91.74084624 Axis 0.08520945 -0.89041639 0.44709954 Axis point 288.89173644 0.00000000 170.82623441 Rotation angle (degrees) 24.51047046 Shift along axis 8.16414932 > hide #5 models > show #5 models > hide #5 models > show #5 models > vop gaussian #4 sdev 1.96 Opened emdb 12873 gaussian as #6, grid size 480,480,480, pixel 0.652, shown at step 1, values float32 > hide #5 models > view orient > show #5 models > hide #5 models > show #5 models > hide #5 models > show #5 models > ui mousemode right ""move picked models"" > view matrix models > #5,0.91054,-0.19232,-0.36596,82.079,0.17865,0.98133,-0.071225,-79.04,0.37283,-0.00052507,0.9279,-116.54 > fitmap #5 inMap #6 Fit molecule 7oe2 (#5) to map emdb 12873 gaussian (#6) using 10589 atoms average map value = 0.004612, steps = 200 shifted from previous position = 16.8 rotated from previous position = 16.7 degrees atoms outside contour = 9560, contour level = 0.0073394 Position of 7oe2 (#5) relative to emdb 12873 gaussian (#6) coordinates: Matrix rotation and translation 0.97774690 -0.00930949 -0.20958134 12.02272988 0.03648857 0.99133437 0.12619334 -56.63541392 0.20659038 -0.13103247 0.96961379 -43.91896589 Axis -0.52346857 -0.84693218 0.09320157 Axis point 247.91471428 0.00000000 124.90403528 Rotation angle (degrees) 14.22282997 Shift along axis 37.57951693 > hide #5 models > show #5 models > hide #5 models > show #5 models > close #6 > volume gaussian #4 sDev 5 Opened emdb 12873 gaussian as #6, grid size 480,480,480, pixel 0.652, shown at step 1, values float32 > volume #6 level 0.003765 > fitmap #5 inMap #6 Fit molecule 7oe2 (#5) to map emdb 12873 gaussian (#6) using 10589 atoms average map value = 0.004506, steps = 404 shifted from previous position = 9.65 rotated from previous position = 31.8 degrees atoms outside contour = 1664, contour level = 0.0037647 Position of 7oe2 (#5) relative to emdb 12873 gaussian (#6) coordinates: Matrix rotation and translation 0.98828342 0.12412747 -0.08881588 -36.40669678 -0.14825672 0.91899735 -0.36532701 80.16530233 0.03627444 0.37421417 0.92663257 -93.87496277 Axis 0.92677398 -0.15675997 -0.34134485 Axis point 0.00000000 292.95641979 148.35768660 Rotation angle (degrees) 23.51485417 Shift along axis -14.26375421 > volume #6 level 0.004316 > hide #!6 models > clip > hide #!4 models > show #!6 models > volume #6 level 0.003405 > ui mousemode right clip > volume #6 level 0.004347 > help vol gauss > close #6 > volume gaussian #4 sDev 3 step 4 Opened emdb 12873 gaussian as #6, grid size 120,120,120, pixel 2.61, shown at step 1, values float32 > volume #6 level 0.003896 > ui mousemode right ""pick blobs"" > measure blob #!6.1 triangleNumber 70394 color #0000ccff outline true Surface emdb 12873 gaussian #6.1 blob: volume = 78705 area = 15620 size = 78.554 66.674 42.089 > measure blob #!6.1 triangleNumber 152159 color #1ffd0bff Surface emdb 12873 gaussian #6.1 blob: volume = 83180 area = 15251 size = 79.229 68.325 42.064 > measure blob #!6.1.1 triangleNumber 2051 color #da0885ff Surface cap front #6.1.1 blob: volume = 0.00027329 (1 holes) area = 81.723 size = 17.46 7.3457 0.013351 boundary = 48.857 > measure blob #!6.1 triangleNumber 131265 color #5c8dc0ff Surface emdb 12873 gaussian #6.1 blob: volume = 54398 area = 13406 size = 68.215 66.896 38.139 > measure blob #!6.1 triangleNumber 134826 color #4bcf81ff Surface emdb 12873 gaussian #6.1 blob: volume = 82961 area = 15802 size = 82.047 68.507 42.295 > measure blob #!6.1 triangleNumber 13368 color #98a47aff Surface emdb 12873 gaussian #6.1 blob: volume = 2.2105e+06 area = 3.9482e+05 size = 235.6 234.21 241.1 > open 5n5f format mmcif fromDatabase pdb 5n5f title: Crystal structure of Haliangium ochraceum encapsulated ferritin [more info...] Chain information for 5n5f #7 --- Chain | Description | UniProt A B C D E F G H I J | encapsulated ferritin | D0LZ73_HALO1 Non-standard residues in 5n5f #7 --- NA — sodium ion > ui mousemode right ""move picked models"" > view matrix models #7,1,0,0,118.84,0,1,0,106.24,0,0,1,-92.01 > lighting simple > view matrix models #7,1,0,0,193.89,0,1,0,196.86,0,0,1,9.9052 > view matrix models #7,1,0,0,191.91,0,1,0,179.73,0,0,1,10.296 > hide #5 models > fitmap #7 inMap #6 Fit molecule 5n5f (#7) to map emdb 12873 gaussian (#6) using 15189 atoms average map value = 0.002953, steps = 96 shifted from previous position = 12.8 rotated from previous position = 38.1 degrees atoms outside contour = 10606, contour level = 0.0038961 Position of 5n5f (#7) relative to emdb 12873 gaussian (#6) coordinates: Matrix rotation and translation 0.79420998 -0.17641893 -0.58146957 281.59908754 0.10003328 0.98182972 -0.16125679 199.41346375 0.59935286 0.06990545 0.79742672 47.85089785 Axis 0.18723862 -0.95645189 0.22392294 Axis point 44.78580067 0.00000000 509.42629818 Rotation angle (degrees) 38.11873553 Shift along axis -127.28824487 > show #5 models > hide #!6 models > clip false Expected a keyword > clip off > open /Users/goddard/ucsf/presentations/vr-nih- > feb2022/data/alphafold_uniprot_D0LZ73.pdb Summary of feedback from opening /Users/goddard/ucsf/presentations/vr-nih- feb2022/data/alphafold_uniprot_D0LZ73.pdb --- warning | Ignored bad PDB record found on line 2026 Chain information for alphafold_uniprot_D0LZ73.pdb #8 --- Chain | Description A | No description available > mmaker #8 to #7/G Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 5n5f, chain G (#7) with alphafold_uniprot_D0LZ73.pdb, chain A (#8), sequence alignment score = 487.4 RMSD between 92 pruned atom pairs is 0.443 angstroms; (across all 92 pairs: 0.443) > close #3 > close #1 > close #2 > lighting soft > show #8 > save /Users/goddard/ucsf/presentations/vr-nih-feb2022/data/ferritin.cxs > ui tool show ""Show Sequence Viewer"" > sequence chain #8 Alignment identifier is 8/A > select #8/A:117 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/A:117-125 124 atoms, 123 bonds, 9 residues, 1 model selected > color sel magenta > color sel byhetero > select clear > save /Users/goddard/ucsf/presentations/vr-nih-feb2022/data/ferritin.cxs ——— End of log from Tue Feb 15 17:17:52 2022 ——— opened ChimeraX session > ui mousemode right tug OpenGL version: 4.1 ATI-4.7.29 OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine OpenGL vendor: ATI Technologies Inc. Locale: UTF-8 Qt version: PyQt5 5.15.2, Qt 5.15.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac18,3 Processor Name: Quad-Core Intel Core i7 Processor Speed: 4.2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 447.40.12.0.0 OS Loader Version: 540.40.4~45 SMC Version (system): 2.41f2 Software: System Software Overview: System Version: macOS 12.0.1 (21A559) Kernel Version: Darwin 21.1.0 Time since boot: 110 days 21 minutes Graphics/Displays: Radeon Pro 580: Chipset Model: Radeon Pro 580 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x67df Revision ID: 0x00c0 ROM Revision: 113-D000AA-931 VBIOS Version: 113-D0001A1X-025 EFI Driver Version: 01.00.931 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.5.30 cftime: 1.5.2 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.36.2 ChimeraX-AtomicLibrary: 6.0.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.1 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4.dev202202151837 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 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: 2.1.2 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: 1.1.5 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: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.1 ChimeraX-ModelPanel: 1.3.2 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: 1.8 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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: 2.4.6 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: 1.7.7 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.16 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.1 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 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.5.1 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.29.1 funcparserlib: 1.0.0a0 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.26 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.9.2 kiwisolver: 1.3.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.0.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.4 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.0 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.28 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.7 PyQt5: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.2.2 QtPy: 2.0.1 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 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-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.8 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Structure Editing fixed all ChimeraX