Startup warning: Replacing fetcher for pdb_nmr and format NMRSTAR...
The following bug report has been submitted:
Platform: macOS-14.3.1-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Why am I getting this warning about "Replacing fetcher for pdb_nmr and format NMRSTAR..." in the log at startup? I added a toolshed bundle NMRSTAR that defines these things but I don't even have them installed. It is not in ChimeraX 1.7.1. This annoying warning has appeared in 69 bug reports since January 18, 2024 when I added the Toolshed bundle. Apparently just checking for Toolshed bundles is causing it.
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> toolshed list
List of installed bundles:
* AddCharge (1.5.13): Add partial charges to atoms
* AddH (2.2.5): Add hydrogens
* AlignmentAlgorithms (2.0.1): Sequence alignment algorithms
* AlignmentHdrs (3.4.1): Alignment header support
* AlignmentMatrices (2.1): Sequence alignment similarity matrices
* Alignments (2.12.2): Sequence alignment support
* AlphaFold (1.0): Predict or fetch AlphaFold structures
* AltlocExplorer (1.1.1): Examine/change alternate atomic locations
* AmberInfo (1.0): Provide information about AmberTools installation
* Arrays (1.1): C++ library for parsing numpy arrays
* Atomic (1.49.1): Atomic-structure functionality
* AtomicLibrary (12.1.5): Atomic-structure C++ library
* AtomSearch (2.0.1): 3D atom search
* AxesPlanes (2.3.2): Depict axes or planes
* BasicActions (1.1.2): Basic actions for user-defined specifier names
* BILD (1.0): BILD file reader
* BlastProtein (2.1.2): Search PDB/NR/AlphaFold using BLAST
* BondRot (2.0.4): Bond rotation support
* BugReporter (1.0.1): Report bugs when an error occurs
* BuildStructure (2.10.5): Create/modify structures
* Bumps (1.0): Find protrusions in density maps
* ButtonPanel (1.0.1): Create custom user interface panels
* CageBuilder (1.0.1): Build polygonal meshes for oligomeric molecular assemblies
* CellPack (1.0): Fetch cellPACK models from web
* Centroids (1.3.2): Depict centroid of atoms
* ChangeChains (1.1): Change chain IDs
* CheckWaters (1.3.2): Check water placement in maps
* ChemGroup (2.0.1): Detect chemically functional groups
* Clashes (2.2.4): Find clashes/contacts in structures
* Clipper (0.22.3): Clipper: Efficient handling of volumetric data and symmetry
* ColorActions (1.0.3): Simple interface for coloring objects
* ColorGlobe (1.0): Show directional resolution colored sphere
* ColorKey (1.5.5): Add color key to graphics
* CommandLine (1.2.5): Command line support
* ConnectStructure (2.0.1): Add bonds to structures that lack them
* Contacts (1.0.1): Display chain contact maps
* Core (1.7.1): ChimeraX Core Package
* CoreFormats (1.2): ChimeraX session support
* coulombic (1.4.2): Compute/show electrostatic potential
* Crosslinks (1.0): Analyze crosslinks
* Crystal (1.0): Crystal symmetries
* CrystalContacts (1.0.1): Show contacting asymmetric units in a crystal
* DataFormats (1.2.3): Data format management
* Dicom (1.2): Read medical imaging and segmentations in DICOM format
* DistMonitor (1.4): Interactive distance display
* DockPrep (1.1.3): Prepare structures for docking
* Dssp (2.0): Compute/assign secondary structure
* EMDB-SFF (1.0): EMDB SFF file reader
* ESMFold (1.0): Predict or fetch ESMFold structures
* FileHistory (1.0.1): File History Panel
* FunctionKey (1.0.1): Assign function keys to run commands
* Geometry (1.3): Vector and coordinate system routines
* gltf (1.0): Read/write glTF 3d scene files
* Graphics (1.1.1): OpenGL graphics rendering
* Hbonds (2.4): Identify hydrogen bonds in and among structures
* Help (1.2.2): Show ChimeraX Help
* HKCage (1.3): Create icosahedral mesh of hexagons and pentagons
* IHM (1.1): Integrative Hybrid Models file reader
* ImageFormats (1.2): Support for saving images
* IMOD (1.0): IMOD model file reader
* IO (1.0.1): Python convenience input/output functions
* ISOLDE (1.7): ISOLDE: Interactive Structure Optimisation by Local Direct Exploration
* ItemsInspection (1.0.1): Inspection of attributes of a set of items
* IUPAC (1.0): IUPAC fetch
* Label (1.1.8): Add text labels to graphics
* ListInfo (1.2.2): Report attributes for selected atomic data
* Log (1.1.6): Log support
* LookingGlass (1.1): LookingGlass holographic display
* Maestro (1.9.1): Maestro reader
* Map (1.1.4): Density maps
* MapData (2.0): Volume data file formats
* MapEraser (1.0.1): Map eraser
* MapFilter (2.0.1): Operations on maps
* MapFit (2.0): Fit molecules into maps
* MapSeries (2.1.1): Volume series
* Markers (1.0.1): Place markers on density maps
* Mask (1.0.2): Mask a volume to a surface
* MatchMaker (2.1.2): Superimpose structures
* MCopy (1.0): Copy atomic structure attributes to another structure
* MDcrds (2.6.1): Molecular dynamics support
* MedicalToolbar (1.0.2): Toolbar for medical image analysis
* Meeting (1.0.1): Shared interactive VR sessions.
* MLP (1.1.1): Molecular lipophilicity calculation
* mmCIF (2.12.1): mmCIF format read/write
* MMTF (2.2): MMTF format read/write
* Modeller (1.5.14): Interface to Modeller
* ModelPanel (1.4): ChimeraX Model Panel
* ModelSeries (1.0.1): Display sequences of models one by one
* Mol2 (2.0.3): Mol2 reader/writer
* Mole (1.0): Open JSON tunnel files from Mole
* Morph (1.0.2): Morph atomic structures
* MouseModes (1.2): Provide right button mouse mode tool
* Movie (1.0): Commands to record movies
* Neuron (1.0): Read SWC neuron trace files
* Nifti (1.1): Read medical images in NIfTI format
* NIHPresets (1.1.15): NIH3D presets
* NRRD (1.1): Read medical images in NRRD format
* Nucleotides (2.0.3): Create nucleotide-specific displays
* OpenCommand (1.13.1): Manages 'open' command extensibility
* PDB (2.7.3): PDB format read/write
* PDBBio (1.0.1): PDB biological assembly fetch
* PDBLibrary (1.0.4): C++ PDB support
* PDBMatrices (1.0): Crystal and biological unit matrices
* PhenixUI (1.2.0): Run model bulding calculations using Phenix
* PickBlobs (1.0.1): Measure and color blobs
* Positions (1.0): Read and write model position matrices
* PresetMgr (1.1): Preset management
* PubChem (2.1): PubChem fetch
* ReadPbonds (1.0.1): Read in pseudobonds from a file
* Registration (1.1.2): Register ChimeraX
* RemoteControl (1.0): Control ChimeraX from other apps
* RenderByAttr (1.1): Depict attribute values on structures
* RenumberResidues (1.1): Renumber residues
* ResidueFit (1.0.1): Display fit of residues to density map
* RestServer (1.2): Starts REST server to execute commands from network requests
* RNALayout (1.0): Make RNA models
* RotamerLibMgr (4.0): Manage rotamer libraries
* RotamerLibsDunbrack (2.0): Dunbrack rotamer library
* RotamerLibsDynameomics (2.0): Dynameomics rotamer library
* RotamerLibsRichardson (2.0): Richardson rotamer libraries
* SaveCommand (1.5.1): Manages 'save' command extensibility
* SchemeMgr (1.0): HTTP scheme management
* SDF (2.0.2): SDF file reader
* Segger (1.0): Segment map
* Segment (1.0.1): Watershed segment calculation
* SelInspector (1.0): Inspect contents of selection
* SeqView (2.11): Sequence viewer
* Shape (1.0.1): Make models for geometric shapes
* Shell (1.0.1): Interactive Python shell
* Shortcuts (1.1.1): Button and keyboard shortcuts
* ShowSequences (1.0.2): Choose/show structure sequences
* SideView (1.0.1): Side view of scene
* Smiles (2.1.2): SMILES fetch
* SmoothLines (1.0): Smooth network of lines
* SpaceNavigator (1.0): Space Navigator device support
* StdCommands (1.12.4): Standard commands
* STL (1.0.1): STL file read/write
* Storm (1.0): STORM file reader
* StructMeasure (1.1.2): Structure measurement user interface
* Struts (1.0.1): struts for 3D printing
* Surface (1.0.1): Surface calculations
* SwapAA (2.0.1): Swap amino acid
* SwapRes (2.2.2): Swap residue side chains
* TapeMeasure (1.0): Tape measure mouse mode
* TaskManager (1.0): Manage background tasks in ChimeraX
* Test (1.0): simple regression test
* TetraScapeCommand (0.1): Low Poly Protein Design using Tetrahedrons
* Toolbar (1.1.2): Toolbar
* ToolshedUtils (1.2.4): Toolshed bundle utilities
* Topography (1.0): Show a topographic surface for a 2D image
* ToQuest (1.0): Copy scenes to VR Quest headset
* Tug (1.0.1): Tug on atoms with molecular dynamics
* UI (1.33.3): ChimeraX user interface
* uniprot (2.3): UniProt database support
* UnitCell (1.0.1): Show crystal unit cell
* ViewDockX (1.3.2): Analyze ligand-receptor docking results
* VIPERdb (1.0): Read Virus Particle Explorer .vdb files
* Vive (1.1): Virtual reality headset support
* VolumeMenu (1.0.1): Volume menu
* vrml (1.0): Write basic VRML output for 3D color printing
* VTK (1.0): Legacy VTK file reader and writer
* WavefrontOBJ (1.0): Wavefront OBJ file read/write
* WebCam (1.0.2): Combine camera video with graphics
* WebServices (1.1.3): Web service and HTTP request support
* Zone (1.0.1): Mouse mode to show atom and map zones
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac14,14
Model Number: Z1800003VLL/A
Chip: Apple M2 Ultra
Total Number of Cores: 24 (16 performance and 8 efficiency)
Memory: 64 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3.1 (23D60)
Kernel Version: Darwin 23.3.0
Time since boot: 14 days, 8 hours, 50 minutes
Graphics/Displays:
Apple M2 Ultra:
Chipset Model: Apple M2 Ultra
Type: GPU
Bus: Built-In
Total Number of Cores: 60
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
PHL 278B1:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
alphashape: 1.3.1
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.3
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.7
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NIHPresets: 1.1.15
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.2.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-TetraScapeCommand: 0.1
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
click: 8.1.7
click-log: 0.4.0
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynmrstar: 3.3.2
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
Rtree: 1.1.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
shapely: 2.0.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
trimesh: 4.0.10
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Would be good if you can take a look at this in the next few weeks. If it is not resolved by then I will delete the NMRSTAR bundle from the Toolshed so our users are not annoyed by this.