Allow different case for fetch database name

[chimerax-bug-report@…]

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