Opened 3 years ago
Closed 3 years ago
#8295 closed defect (fixed)
Allow different case for fetch database name
Reported by: | Owned by: | Eric Pettersen | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Input/Output | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open > /Users/nganga/Desktop/Peter_Njenga/012_PUBLICATIONS/001_Tc_Kinetics_paper/004_Figure- > data/ChimeraX_sessions/WT_Pore_intermediate.cxs format session Opened WT_DR_locres_Job013.mrc as #1, grid size 384,384,384, pixel 0.88, shown at level 0.0156, step 1, values float32 Opened difference_class1minusfullmap10A.mrc as #2, grid size 384,384,384, pixel 0.87, shown at level 1.16, step 1, values float32 Log from Tue Sep 13 16:42:39 2022UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open "/Users/nganga/Desktop/Peter_Njenga/012_PUBLICATIONS/001_Tc Kinetics > paper/Figure-data/WT_DR_improved/WT_DR_locres_Job013.mrc" format mrc No such file/path: /Users/nganga/Desktop/Peter_Njenga/012_PUBLICATIONS/001_Tc Kinetics paper/Figure-data/WT_DR_improved/WT_DR_locres_Job013.mrc > open > /Users/nganga/Desktop/Peter_Njenga/012_PUBLICATIONS/001_Tc_Kinetics_paper/Figure- > data/WT_DR_improved/WT_DR_locres_Job013.mrc Opened WT_DR_locres_Job013.mrc as #1, grid size 384,384,384, pixel 0.88, shown at level 0.0233, step 2, values float32 > volume #1 step 1 > open > /Users/nganga/Desktop/Peter_Njenga/012_PUBLICATIONS/001_Tc_Kinetics_paper/Figure- > data/WT_DR_improved/difference_class1minusfullmap10A.mrc Opened difference_class1minusfullmap10A.mrc as #2, grid size 384,384,384, pixel 0.87, shown at level 0.321, step 2, values float32 > volume #2 step 1 > volume #2 level 1.07 > volume #2 level 1.422 > volume #2 level 1.273 > volume #2 level 1.164 > open > /Users/nganga/Desktop/Peter_Njenga/012_PUBLICATIONS/001_Tc_Kinetics_paper/Figure- > data/WT_DR_improved/TcdA1_DR_WT_pentamer_Isolde_full.pdb Chain information for TcdA1_DR_WT_pentamer_Isolde_full.pdb #3 --- Chain | Description A B C D E | No description available > select #3 84390 atoms, 86195 bonds, 10610 residues, 1 model selected > cartoon sel > hide sel target a > color #3/A:1-2600 red > color #3/B:1-2600 coral > color #3/C:1-2600 khaki > color #3/D:1-2600 forestgreen > color #3/E:1-2600 goldenrod Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 1 atomic models, 2 maps. > select #1 2 models selected > select #3 84390 atoms, 86195 bonds, 10610 residues, 1 model selected > select #1 2 models selected > select #3 84390 atoms, 86195 bonds, 10610 residues, 1 model selected > ~select #3 Nothing selected > ui tool show "Fit in Map" Fit molecule TcdA1_DR_WT_pentamer_Isolde_full.pdb (#3) to map WT_DR_locres_Job013.mrc (#1) using 84390 atoms average map value = 0.02972, steps = 40 shifted from previous position = 0.0107 rotated from previous position = 0.00611 degrees atoms outside contour = 35879, contour level = 0.023277 Position of TcdA1_DR_WT_pentamer_Isolde_full.pdb (#3) relative to WT_DR_locres_Job013.mrc (#1) coordinates: Matrix rotation and translation 0.99999999 0.00010507 0.00001705 -0.01991788 -0.00010507 0.99999999 0.00000510 0.01712124 -0.00001705 -0.00000510 1.00000000 0.01441724 Axis -0.04782906 0.16001250 -0.98595557 Axis point 178.97291729 194.37565389 0.00000000 Rotation angle (degrees) 0.00610556 Shift along axis -0.01052249 Fit molecule TcdA1_DR_WT_pentamer_Isolde_full.pdb (#3) to map WT_DR_locres_Job013.mrc (#1) using 84390 atoms average map value = 0.02972, steps = 28 shifted from previous position = 0.00649 rotated from previous position = 0.00242 degrees atoms outside contour = 35886, contour level = 0.023277 Position of TcdA1_DR_WT_pentamer_Isolde_full.pdb (#3) relative to WT_DR_locres_Job013.mrc (#1) coordinates: Matrix rotation and translation 1.00000000 0.00006927 0.00002789 -0.01589292 -0.00006927 1.00000000 -0.00001448 0.01604247 -0.00002789 0.00001447 1.00000000 0.01915673 Axis 0.19031484 0.36670334 -0.91066400 Axis point 308.82186730 189.37654115 0.00000000 Rotation angle (degrees) 0.00435805 Shift along axis -0.01458717 > volume #1 level 0.01387 > volume #1 level 0.01561 > ui tool show "Color Zone" > color zone #1 near #3 distance 2.31 > color zone #1 near #3 distance 2.2 > color zone #1 near #3 distance 3.02 > color zone #1 near #3 distance 2.98 > color zone #1 near #3 distance 3.62 > color zone #1 near #3 distance 3.79 > color zone #1 near #3 distance 3.96 > color zone #1 near #3 distance 3.68 > color zone #1 near #3 distance 4.21 > color zone #1 near #3 distance 4.02 > color zone #1 near #3 distance 4.4 > color zone #1 near #3 distance 4.02 > color zone #1 near #3 distance 4.82 > color zone #1 near #3 distance 4.68 > color zone #1 near #3 distance 4.21 > color zone #1 near #3 distance 4 [Repeated 1 time(s)] > color #3/A:1-2600 red > color #3/B:1-2600 coral > color #3/C:1-2600 khaki > color #3/D:1-2600 forestgreen > color #3/E:1-2600 goldenrod > hide #3 models > toolshed show > volume style surface > lighting simple > lighting full > lighting soft > lighting full > lighting soft > color zone #1 near #3 distance 4.1 [Repeated 1 time(s)] > color #3/A:1-2600 red > color #3/B:1-2600 coral > color #3/C:1-2600 khaki > color #3/D:1-2600 forestgreen > color #3/E:1-2600 goldenrod > color zone #1 near #3 distance 4.2 [Repeated 1 time(s)] > color #3/A:1-2600 red > color #3/B:1-2600 coral > color #3/C:1-2600 khaki > color #3/D:1-2600 forestgreen > color #3/E:1-2600 goldenrod > select #2 2 models selected > color #2 #ffaa28 models transparency 0 > ~select #2 Nothing selected > color #2 #f6c255 models transparency 0 > color #2 #f6be54 models transparency 0 > color zone #1 near #3 distance 4.4 [Repeated 1 time(s)] > color #3/A:1-2600 red > color #3/B:1-2600 coral > color #3/C:1-2600 khaki > color #3/D:1-2600 forestgreen > color #3/E:1-2600 goldenrod > color zone #1 near #3 distance 4.8 [Repeated 1 time(s)] > color #3/A:1-2600 red > color #3/B:1-2600 coral > color #3/C:1-2600 khaki > color #3/D:1-2600 forestgreen > color #3/E:1-2600 goldenrod > color zone #1 near #3 distance 5 [Repeated 1 time(s)] > color #3/A:1-2600 red > color #3/B:1-2600 coral > color #3/C:1-2600 khaki > color #3/D:1-2600 forestgreen > color #3/E:1-2600 goldenrod > set bgColor white > ui tool show "Hide Dust" > surface dust #1 size 5.28 > save > /Users/nganga/Desktop/Peter_Njenga/012_PUBLICATIONS/001_Tc_Kinetics_paper/Figure- > data/ChimeraX_sessions/WT_Pore_intermediate.cxs ——— End of log from Tue Sep 13 16:42:39 2022 ——— opened ChimeraX session > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > close #2 > show #3 models > hide #!1 models > show #!1 models > open EMDB 10033 'EMDB' has no suffix > open EMDB:10033 Traceback (most recent call last): File "/Volumes/ChimeraXInstaller/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/cmd_line/tool.py", line 297, in execute cmd.run(cmd_text) File "/Volumes/ChimeraXInstaller/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py", line 2856, in run result = ci.function(session, **kw_args) File "/Volumes/ChimeraXInstaller/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py", line 71, in cmd_open provider_args = mgr.fetch_args(fetches[0][1], format_name=fetches[0][2]) File "/Volumes/ChimeraXInstaller/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/manager.py", line 170, in fetch_args args.update(provider_info.bundle_info.run_provider(self.session, File "/Volumes/ChimeraXInstaller/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py", line 381, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File "/Volumes/ChimeraXInstaller/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py", line 1284, in run_provider return cls._get_func(api, "run_provider")(session, name, mgr, **kw) File "/Volumes/ChimeraXInstaller/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map/__init__.py", line 165, in run_provider class Info(OpenerInfo): File "/Volumes/ChimeraXInstaller/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map/__init__.py", line 167, in Info _name=session.data_formats[name].nicknames[0], **kw): File "/Volumes/ChimeraXInstaller/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/data_formats/manager.py", line 145, in __getitem__ raise KeyError("No known data format '%s'" % key) KeyError: "No known data format 'EMDB'" KeyError: "No known data format 'EMDB'" File "/Volumes/ChimeraXInstaller/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/data_formats/manager.py", line 145, in __getitem__ raise KeyError("No known data format '%s'" % key) See log for complete Python traceback. OpenGL version: 4.1 ATI-4.8.101 OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac18,3 Processor Name: Quad-Core Intel Core i5 Processor Speed: 3.8 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Memory: 16 GB System Firmware Version: 451.140.1.0.0 OS Loader Version: 540.120.3~22 SMC Version (system): 2.41f2 Software: System Software Overview: System Version: macOS 12.6 (21G115) Kernel Version: Darwin 21.6.0 Time since boot: 37 days 4:29 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 EV2455: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 Framebuffer Depth: 30-Bit Color (ARGB2101010) Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort 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: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 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: 1.31 ChimeraX-AtomicLibrary: 4.2 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: 2.6.1 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 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 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-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: 2.1.2 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: 1.1.4 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: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 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: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 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: 1.6.1 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: 1.13.7 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 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 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: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
Component: | Unassigned → Input/Output |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → Allow different case for fetch database name |
comment:2 by , 3 years ago
Resolution: | → fixed |
---|---|
Status: | accepted → closed |
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