Opened 16 months ago

Last modified 16 months ago

#15492 assigned defect

Duplicate bundles in cache

Reported by: Zach Pearson Owned by: Zach Pearson
Priority: moderate Milestone:
Component: Tool Shed Version:
Keywords: Cc: Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

I built ChimeraX from scratch then tried to install the graphics bundle in editable mode. After installing, I started ChimeraX from the command line ./ChimeraX.app/Contents/bin/python3.11 -I -m chimerax.core and got the following output: 

WARNING: QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "help" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "basicactions" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "installable" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "vdxchart" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "vdxplot" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "vdxtable" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "cxreg" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "help" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "cxcmd" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "help" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "basicactions" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "vdxchart" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "vdxplot" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "vdxtable" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "cxreg" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "installable" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "basicactions" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "installable" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "vdxchart" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "vdxplot" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "vdxtable" already registered
WARNING: QWebEngineUrlScheme::registerScheme: Scheme "cxreg" already registered
NOTE: Replacing data format 'IMOD model' as defined by ChimeraX-IMOD with definition from ChimeraX-IMOD
NOTE: Replacing data format 'VRML' as defined by ChimeraX-vrml with definition from ChimeraX-vrml
NOTE: Replacing data format 'Amira mesh' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'APBS potential' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'BRIX density map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'CCP4 density map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'Chimera map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'CNS or XPLOR density map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'DelPhi or GRASP potential' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'DeltaVision map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'DSN6 density map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'DOCK scoring grid' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'EMAN HDF map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'Gaussian cube grid' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'gOpenMol grid' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'HDF map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'Image stack' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'ImageJ TIFF map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'IMAGIC density map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'Imaris map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'IMOD map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'MacMolPlt grid' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'MRC density map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'NetCDF map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'Priism microscope image' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'PROFEC free energy grid' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'Purdue image format' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'SITUS map file' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'SPIDER volume data' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'TOM toolbox EM density map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'UHBD grid, binary' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'EMDB SFF' as defined by ChimeraX-EMDB-SFF with definition from ChimeraX-EMDB-SFF
NOTE: Replacing data format 'VIPERdb' as defined by ChimeraX-VIPERdb with definition from ChimeraX-VIPERdb
NOTE: Replacing data format 'Wavefront OBJ' as defined by ChimeraX-WavefrontOBJ with definition from ChimeraX-WavefrontOBJ
NOTE: Replacing data format 'DiffPlot' as defined by ChimeraX-DiffPlot with definition from ChimeraX-DiffPlot
NOTE: Replacing data format 'IUPAC' as defined by ChimeraX-IUPAC with definition from ChimeraX-IUPAC
NOTE: Replacing data format 'Model Positions' as defined by ChimeraX-Positions with definition from ChimeraX-Positions
NOTE: Replacing data format 'Pseudobonds' as defined by ChimeraX-ReadPbonds with definition from ChimeraX-ReadPbonds
NOTE: Replacing data format 'NRRD Medical Imaging' as defined by ChimeraX-NRRD with definition from ChimeraX-NRRD
NOTE: Replacing data format 'define attribute' as defined by ChimeraX-StdCommands with definition from ChimeraX-StdCommands
NOTE: Replacing data format 'Schrodinger Maestro' as defined by ChimeraX-Maestro with definition from ChimeraX-Maestro
NOTE: Replacing data format 'UniProt sequence' as defined by ChimeraX-uniprot with definition from ChimeraX-uniprot
NOTE: Replacing data format 'Deep mutational scan' as defined by ChimeraX-DeepMutationalScan with definition from ChimeraX-DeepMutationalScan
NOTE: Replacing data format 'STORM microscopy' as defined by ChimeraX-Storm with definition from ChimeraX-Storm
NOTE: Replacing data format 'HTML' as defined by ChimeraX-Help with definition from ChimeraX-Help
NOTE: Replacing data format 'PDB' as defined by ChimeraX-PDB with definition from ChimeraX-PDB
NOTE: Replacing data format 'cellpack' as defined by ChimeraX-CellPack with definition from ChimeraX-CellPack
NOTE: Replacing data format 'ChimeraX session' as defined by ChimeraX-CoreFormats with definition from ChimeraX-CoreFormats
NOTE: Replacing data format 'ChimeraX commands' as defined by ChimeraX-CoreFormats with definition from ChimeraX-CoreFormats
NOTE: Replacing data format 'Python' as defined by ChimeraX-CoreFormats with definition from ChimeraX-CoreFormats
NOTE: Replacing data format 'Compiled Python' as defined by ChimeraX-CoreFormats with definition from ChimeraX-CoreFormats
NOTE: Replacing data format 'X3D' as defined by ChimeraX-CoreFormats with definition from ChimeraX-CoreFormats
NOTE: Replacing data format 'web fetch' as defined by ChimeraX-CoreFormats with definition from ChimeraX-CoreFormats
NOTE: Replacing data format 'NIfTI Medical Imaging' as defined by ChimeraX-Nifti with definition from ChimeraX-Nifti
NOTE: Replacing data format 'Gromacs full-precision coordinates' as defined by ChimeraX-MDcrds with definition from ChimeraX-MDcrds
NOTE: Replacing data format 'Gromacs compressed coordinates' as defined by ChimeraX-MDcrds with definition from ChimeraX-MDcrds
NOTE: Replacing data format 'DCD coordinates' as defined by ChimeraX-MDcrds with definition from ChimeraX-MDcrds
NOTE: Replacing data format 'Amber netCDF coordinates' as defined by ChimeraX-MDcrds with definition from ChimeraX-MDcrds
NOTE: Replacing data format 'Gromos87 coordinates' as defined by ChimeraX-MDcrds with definition from ChimeraX-MDcrds
NOTE: Replacing data format 'Protein structure file' as defined by ChimeraX-MDcrds with definition from ChimeraX-MDcrds
NOTE: Replacing data format 'AlphaFold PAE' as defined by ChimeraX-AlphaFold with definition from ChimeraX-AlphaFold
NOTE: Replacing data format 'Macromolecular Transmission' as defined by ChimeraX-MMTF with definition from ChimeraX-MMTF
NOTE: Replacing data format 'Sybyl Mol2' as defined by ChimeraX-Mol2 with definition from ChimeraX-Mol2
NOTE: Replacing data format 'Marker model' as defined by ChimeraX-Markers with definition from ChimeraX-Markers
NOTE: Replacing data format 'NMRSTAR' as defined by ChimeraX-NMRSTAR with definition from ChimeraX-NMRSTAR
NOTE: Replacing data format 'GL Transmission' as defined by ChimeraX-gltf with definition from ChimeraX-gltf
NOTE: Replacing data format 'AutoDock PDBQT' as defined by ChimeraX-ViewDockX with definition from ChimeraX-ViewDockX
NOTE: Replacing data format 'ZDOCK' as defined by ChimeraX-ViewDockX with definition from ChimeraX-ViewDockX
NOTE: Replacing data format 'SwissDock' as defined by ChimeraX-ViewDockX with definition from ChimeraX-ViewDockX
NOTE: Replacing data format 'Bitmap image' as defined by ChimeraX-ImageFormats with definition from ChimeraX-ImageFormats
NOTE: Replacing data format 'Graphics Interchange Format' as defined by ChimeraX-ImageFormats with definition from ChimeraX-ImageFormats
NOTE: Replacing data format 'Joint Photographic Experts Group image' as defined by ChimeraX-ImageFormats with definition from ChimeraX-ImageFormats
NOTE: Replacing data format 'Portable Network Graphics' as defined by ChimeraX-ImageFormats with definition from ChimeraX-ImageFormats
NOTE: Replacing data format 'Portable Pixmap format' as defined by ChimeraX-ImageFormats with definition from ChimeraX-ImageFormats
NOTE: Replacing data format 'Tagged Image File format' as defined by ChimeraX-ImageFormats with definition from ChimeraX-ImageFormats
NOTE: Replacing data format 'photo' as defined by ChimeraX-ImageFormats with definition from ChimeraX-ImageFormats
NOTE: Replacing data format 'Stereolithography' as defined by ChimeraX-STL with definition from ChimeraX-STL
NOTE: Replacing data format 'SWC neurons' as defined by ChimeraX-Neuron with definition from ChimeraX-Neuron
NOTE: Replacing data format 'MDL MOL/SDF' as defined by ChimeraX-SDF with definition from ChimeraX-SDF
NOTE: Replacing data format 'Segmentation' as defined by ChimeraX-Segger with definition from ChimeraX-Segger
NOTE: Replacing data format 'COLLADA' as defined by ChimeraX-Surface with definition from ChimeraX-Surface
NOTE: Replacing data format 'Scalable Vector Graphics' as defined by ChimeraX-Contacts with definition from ChimeraX-Contacts
NOTE: Replacing data format 'Portable Document Format' as defined by ChimeraX-Contacts with definition from ChimeraX-Contacts
NOTE: Replacing data format 'Mole' as defined by ChimeraX-Mole with definition from ChimeraX-Mole
NOTE: Replacing data format 'DICOM medical imaging' as defined by ChimeraX-Dicom with definition from ChimeraX-Dicom
NOTE: Replacing data format 'UCSF Chimera BILD' as defined by ChimeraX-BILD with definition from ChimeraX-BILD
NOTE: Replacing data format 'VTK PolyData' as defined by ChimeraX-VTK with definition from ChimeraX-VTK
NOTE: Replacing data format 'mmCIF' as defined by ChimeraX-mmCIF with definition from ChimeraX-mmCIF
NOTE: Replacing data format 'Chemical Component Dictionary' as defined by ChimeraX-mmCIF with definition from ChimeraX-mmCIF
NOTE: Replacing data format 'Small Molecule CIF' as defined by ChimeraX-mmCIF with definition from ChimeraX-mmCIF
NOTE: Replacing data format 'Crystallography Open Database' as defined by ChimeraX-mmCIF with definition from ChimeraX-mmCIF
NOTE: Replacing data format 'Predicted Crystallography Open Database' as defined by ChimeraX-mmCIF with definition from ChimeraX-mmCIF
NOTE: Replacing data format 'Clustal ALN' as defined by ChimeraX-Alignments with definition from ChimeraX-Alignments
NOTE: Replacing data format 'FASTA' as defined by ChimeraX-Alignments with definition from ChimeraX-Alignments
NOTE: Replacing data format 'HSSP' as defined by ChimeraX-Alignments with definition from ChimeraX-Alignments
NOTE: Replacing data format 'GCG Multiple Sequence File' as defined by ChimeraX-Alignments with definition from ChimeraX-Alignments
NOTE: Replacing data format 'Pfam' as defined by ChimeraX-Alignments with definition from ChimeraX-Alignments
NOTE: Replacing data format 'NBRF/PIR' as defined by ChimeraX-Alignments with definition from ChimeraX-Alignments
NOTE: Replacing data format 'GCG Rich Sequence' as defined by ChimeraX-Alignments with definition from ChimeraX-Alignments
NOTE: Replacing data format 'Stockholm' as defined by ChimeraX-Alignments with definition from ChimeraX-Alignments
NOTE: Replacing data format 'Integrative/Hybrid Models' as defined by ChimeraX-IHM with definition from ChimeraX-IHM
NOTE: Replacing data format 'SMILES' as defined by ChimeraX-Smiles with definition from ChimeraX-Smiles
NOTE: Replacing data format 'Directional FSC' as defined by ChimeraX-ColorGlobe with definition from ChimeraX-ColorGlobe
NOTE: Replacing data format 'IMOD model' as defined by ChimeraX-IMOD with definition from ChimeraX-IMOD
NOTE: Replacing data format 'VRML' as defined by ChimeraX-vrml with definition from ChimeraX-vrml
NOTE: Replacing data format 'Amira mesh' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'APBS potential' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'BRIX density map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'CCP4 density map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'Chimera map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'CNS or XPLOR density map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'DelPhi or GRASP potential' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'DeltaVision map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'DSN6 density map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'DOCK scoring grid' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'EMAN HDF map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'Gaussian cube grid' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'gOpenMol grid' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'HDF map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'Image stack' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'ImageJ TIFF map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'IMAGIC density map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'Imaris map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'IMOD map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'MacMolPlt grid' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'MRC density map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'NetCDF map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'Priism microscope image' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'PROFEC free energy grid' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'Purdue image format' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'SITUS map file' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'SPIDER volume data' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'TOM toolbox EM density map' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'UHBD grid, binary' as defined by ChimeraX-MapData with definition from ChimeraX-MapData
NOTE: Replacing data format 'EMDB SFF' as defined by ChimeraX-EMDB-SFF with definition from ChimeraX-EMDB-SFF
NOTE: Replacing data format 'VIPERdb' as defined by ChimeraX-VIPERdb with definition from ChimeraX-VIPERdb
NOTE: Replacing data format 'Wavefront OBJ' as defined by ChimeraX-WavefrontOBJ with definition from ChimeraX-WavefrontOBJ
NOTE: Replacing data format 'DiffPlot' as defined by ChimeraX-DiffPlot with definition from ChimeraX-DiffPlot
NOTE: Replacing data format 'IUPAC' as defined by ChimeraX-IUPAC with definition from ChimeraX-IUPAC
NOTE: Replacing data format 'Model Positions' as defined by ChimeraX-Positions with definition from ChimeraX-Positions
NOTE: Replacing data format 'Pseudobonds' as defined by ChimeraX-ReadPbonds with definition from ChimeraX-ReadPbonds
NOTE: Replacing data format 'NRRD Medical Imaging' as defined by ChimeraX-NRRD with definition from ChimeraX-NRRD
NOTE: Replacing data format 'define attribute' as defined by ChimeraX-StdCommands with definition from ChimeraX-StdCommands
NOTE: Replacing data format 'Schrodinger Maestro' as defined by ChimeraX-Maestro with definition from ChimeraX-Maestro
NOTE: Replacing data format 'UniProt sequence' as defined by ChimeraX-uniprot with definition from ChimeraX-uniprot
NOTE: Replacing data format 'Deep mutational scan' as defined by ChimeraX-DeepMutationalScan with definition from ChimeraX-DeepMutationalScan
NOTE: Replacing data format 'STORM microscopy' as defined by ChimeraX-Storm with definition from ChimeraX-Storm
NOTE: Replacing data format 'HTML' as defined by ChimeraX-Help with definition from ChimeraX-Help
NOTE: Replacing data format 'PDB' as defined by ChimeraX-PDB with definition from ChimeraX-PDB
NOTE: Replacing data format 'cellpack' as defined by ChimeraX-CellPack with definition from ChimeraX-CellPack
NOTE: Replacing data format 'ChimeraX session' as defined by ChimeraX-CoreFormats with definition from ChimeraX-CoreFormats
NOTE: Replacing data format 'ChimeraX commands' as defined by ChimeraX-CoreFormats with definition from ChimeraX-CoreFormats
NOTE: Replacing data format 'Python' as defined by ChimeraX-CoreFormats with definition from ChimeraX-CoreFormats
NOTE: Replacing data format 'Compiled Python' as defined by ChimeraX-CoreFormats with definition from ChimeraX-CoreFormats
NOTE: Replacing data format 'X3D' as defined by ChimeraX-CoreFormats with definition from ChimeraX-CoreFormats
NOTE: Replacing data format 'web fetch' as defined by ChimeraX-CoreFormats with definition from ChimeraX-CoreFormats
NOTE: Replacing data format 'NIfTI Medical Imaging' as defined by ChimeraX-Nifti with definition from ChimeraX-Nifti
NOTE: Replacing data format 'Gromacs full-precision coordinates' as defined by ChimeraX-MDcrds with definition from ChimeraX-MDcrds
NOTE: Replacing data format 'Gromacs compressed coordinates' as defined by ChimeraX-MDcrds with definition from ChimeraX-MDcrds
NOTE: Replacing data format 'DCD coordinates' as defined by ChimeraX-MDcrds with definition from ChimeraX-MDcrds
NOTE: Replacing data format 'Amber netCDF coordinates' as defined by ChimeraX-MDcrds with definition from ChimeraX-MDcrds
NOTE: Replacing data format 'Gromos87 coordinates' as defined by ChimeraX-MDcrds with definition from ChimeraX-MDcrds
NOTE: Replacing data format 'Protein structure file' as defined by ChimeraX-MDcrds with definition from ChimeraX-MDcrds
NOTE: Replacing data format 'AlphaFold PAE' as defined by ChimeraX-AlphaFold with definition from ChimeraX-AlphaFold
NOTE: Replacing data format 'Macromolecular Transmission' as defined by ChimeraX-MMTF with definition from ChimeraX-MMTF
NOTE: Replacing data format 'Sybyl Mol2' as defined by ChimeraX-Mol2 with definition from ChimeraX-Mol2
NOTE: Replacing data format 'Marker model' as defined by ChimeraX-Markers with definition from ChimeraX-Markers
NOTE: Replacing data format 'NMRSTAR' as defined by ChimeraX-NMRSTAR with definition from ChimeraX-NMRSTAR
NOTE: Replacing data format 'GL Transmission' as defined by ChimeraX-gltf with definition from ChimeraX-gltf
NOTE: Replacing data format 'AutoDock PDBQT' as defined by ChimeraX-ViewDockX with definition from ChimeraX-ViewDockX
NOTE: Replacing data format 'ZDOCK' as defined by ChimeraX-ViewDockX with definition from ChimeraX-ViewDockX
NOTE: Replacing data format 'SwissDock' as defined by ChimeraX-ViewDockX with definition from ChimeraX-ViewDockX
NOTE: Replacing data format 'Bitmap image' as defined by ChimeraX-ImageFormats with definition from ChimeraX-ImageFormats
NOTE: Replacing data format 'Graphics Interchange Format' as defined by ChimeraX-ImageFormats with definition from ChimeraX-ImageFormats
NOTE: Replacing data format 'Joint Photographic Experts Group image' as defined by ChimeraX-ImageFormats with definition from ChimeraX-ImageFormats
NOTE: Replacing data format 'Portable Network Graphics' as defined by ChimeraX-ImageFormats with definition from ChimeraX-ImageFormats
NOTE: Replacing data format 'Portable Pixmap format' as defined by ChimeraX-ImageFormats with definition from ChimeraX-ImageFormats
NOTE: Replacing data format 'Tagged Image File format' as defined by ChimeraX-ImageFormats with definition from ChimeraX-ImageFormats
NOTE: Replacing data format 'photo' as defined by ChimeraX-ImageFormats with definition from ChimeraX-ImageFormats
NOTE: Replacing data format 'Stereolithography' as defined by ChimeraX-STL with definition from ChimeraX-STL
NOTE: Replacing data format 'SWC neurons' as defined by ChimeraX-Neuron with definition from ChimeraX-Neuron
NOTE: Replacing data format 'MDL MOL/SDF' as defined by ChimeraX-SDF with definition from ChimeraX-SDF
NOTE: Replacing data format 'Segmentation' as defined by ChimeraX-Segger with definition from ChimeraX-Segger
NOTE: Replacing data format 'COLLADA' as defined by ChimeraX-Surface with definition from ChimeraX-Surface
NOTE: Replacing data format 'Scalable Vector Graphics' as defined by ChimeraX-Contacts with definition from ChimeraX-Contacts
NOTE: Replacing data format 'Portable Document Format' as defined by ChimeraX-Contacts with definition from ChimeraX-Contacts
NOTE: Replacing data format 'Mole' as defined by ChimeraX-Mole with definition from ChimeraX-Mole
NOTE: Replacing data format 'DICOM medical imaging' as defined by ChimeraX-Dicom with definition from ChimeraX-Dicom
NOTE: Replacing data format 'UCSF Chimera BILD' as defined by ChimeraX-BILD with definition from ChimeraX-BILD
NOTE: Replacing data format 'VTK PolyData' as defined by ChimeraX-VTK with definition from ChimeraX-VTK
NOTE: Replacing data format 'mmCIF' as defined by ChimeraX-mmCIF with definition from ChimeraX-mmCIF
NOTE: Replacing data format 'Chemical Component Dictionary' as defined by ChimeraX-mmCIF with definition from ChimeraX-mmCIF
NOTE: Replacing data format 'Small Molecule CIF' as defined by ChimeraX-mmCIF with definition from ChimeraX-mmCIF
NOTE: Replacing data format 'Crystallography Open Database' as defined by ChimeraX-mmCIF with definition from ChimeraX-mmCIF
NOTE: Replacing data format 'Predicted Crystallography Open Database' as defined by ChimeraX-mmCIF with definition from ChimeraX-mmCIF
NOTE: Replacing data format 'Clustal ALN' as defined by ChimeraX-Alignments with definition from ChimeraX-Alignments
NOTE: Replacing data format 'FASTA' as defined by ChimeraX-Alignments with definition from ChimeraX-Alignments
NOTE: Replacing data format 'HSSP' as defined by ChimeraX-Alignments with definition from ChimeraX-Alignments
NOTE: Replacing data format 'GCG Multiple Sequence File' as defined by ChimeraX-Alignments with definition from ChimeraX-Alignments
NOTE: Replacing data format 'Pfam' as defined by ChimeraX-Alignments with definition from ChimeraX-Alignments
NOTE: Replacing data format 'NBRF/PIR' as defined by ChimeraX-Alignments with definition from ChimeraX-Alignments
NOTE: Replacing data format 'GCG Rich Sequence' as defined by ChimeraX-Alignments with definition from ChimeraX-Alignments
NOTE: Replacing data format 'Stockholm' as defined by ChimeraX-Alignments with definition from ChimeraX-Alignments
NOTE: Replacing data format 'Integrative/Hybrid Models' as defined by ChimeraX-IHM with definition from ChimeraX-IHM
NOTE: Replacing data format 'SMILES' as defined by ChimeraX-Smiles with definition from ChimeraX-Smiles
NOTE: Replacing data format 'Directional FSC' as defined by ChimeraX-ColorGlobe with definition from ChimeraX-ColorGlobe
WARNING: Replacing file-saver for 'VRML' from vrml bundle with that from vrml bundle
WARNING: Replacing file-saver for 'Wavefront OBJ' from WavefrontOBJ bundle with that from WavefrontOBJ bundle
WARNING: Replacing file-saver for 'Model Positions' from Positions bundle with that from Positions bundle
WARNING: Replacing file-saver for 'Pseudobonds' from ReadPbonds bundle with that from ReadPbonds bundle
WARNING: Replacing file-saver for 'NRRD Medical Imaging' from NRRD bundle with that from NRRD bundle
WARNING: Replacing file-saver for 'define attribute' from StdCommands bundle with that from StdCommands bundle
WARNING: Replacing file-saver for 'BRIX density map' from Map bundle with that from Map bundle
WARNING: Replacing file-saver for 'CCP4 density map' from Map bundle with that from Map bundle
WARNING: Replacing file-saver for 'Chimera map' from Map bundle with that from Map bundle
WARNING: Replacing file-saver for 'ImageJ TIFF map' from Map bundle with that from Map bundle
WARNING: Replacing file-saver for 'IMAGIC density map' from Map bundle with that from Map bundle
WARNING: Replacing file-saver for 'MRC density map' from Map bundle with that from Map bundle
WARNING: Replacing file-saver for 'PDB' from PDB bundle with that from PDB bundle
WARNING: Replacing file-saver for 'ChimeraX session' from CoreFormats bundle with that from CoreFormats bundle
WARNING: Replacing file-saver for 'X3D' from CoreFormats bundle with that from CoreFormats bundle
WARNING: Replacing file-saver for 'NIfTI Medical Imaging' from Nifti bundle with that from Nifti bundle
WARNING: Replacing file-saver for 'DCD coordinates' from MDcrds bundle with that from MDcrds bundle
WARNING: Replacing file-saver for 'Sybyl Mol2' from Mol2 bundle with that from Mol2 bundle
WARNING: Replacing file-saver for 'Marker model' from Markers bundle with that from Markers bundle
WARNING: Replacing file-saver for 'GL Transmission' from gltf bundle with that from gltf bundle
WARNING: Replacing file-saver for 'Bitmap image' from ImageFormats bundle with that from ImageFormats bundle
WARNING: Replacing file-saver for 'Graphics Interchange Format' from ImageFormats bundle with that from ImageFormats bundle
WARNING: Replacing file-saver for 'Joint Photographic Experts Group image' from ImageFormats bundle with that from ImageFormats bundle
WARNING: Replacing file-saver for 'Portable Network Graphics' from ImageFormats bundle with that from ImageFormats bundle
WARNING: Replacing file-saver for 'Portable Pixmap format' from ImageFormats bundle with that from ImageFormats bundle
WARNING: Replacing file-saver for 'Tagged Image File format' from ImageFormats bundle with that from ImageFormats bundle
WARNING: Replacing file-saver for 'Stereolithography' from STL bundle with that from STL bundle
WARNING: Replacing file-saver for 'Segmentation' from Segger bundle with that from Segger bundle
WARNING: Replacing file-saver for 'DICOM medical imaging' from Dicom bundle with that from Dicom bundle
WARNING: Replacing file-saver for 'VTK PolyData' from VTK bundle with that from VTK bundle
WARNING: Replacing file-saver for 'mmCIF' from mmCIF bundle with that from mmCIF bundle
WARNING: Replacing file-saver for 'Clustal ALN' from Alignments bundle with that from Alignments bundle
WARNING: Replacing file-saver for 'FASTA' from Alignments bundle with that from Alignments bundle
WARNING: Replacing file-saver for 'NBRF/PIR' from Alignments bundle with that from Alignments bundle
WARNING: Overriding existing toolbar provider for toolbar provider 'Open' in bundle 'ChimeraX-Toolbar'
WARNING: Overriding existing toolbar provider for toolbar provider 'Recent' in bundle 'ChimeraX-Toolbar'
WARNING: Overriding existing toolbar provider for toolbar provider 'Save' in bundle 'ChimeraX-Toolbar'
WARNING: Overriding existing toolbar provider for toolbar provider 'Close' in bundle 'ChimeraX-Toolbar'
WARNING: Overriding existing toolbar provider for toolbar provider 'Exit' in bundle 'ChimeraX-Toolbar'
WARNING: Overriding existing toolbar provider for toolbar provider 'Undo' in bundle 'ChimeraX-Toolbar'
WARNING: Overriding existing toolbar provider for toolbar provider 'Redo' in bundle 'ChimeraX-Toolbar'
WARNING: Overriding existing toolbar provider for toolbar provider 'Side view' in bundle 'ChimeraX-Toolbar'
WARNING: Overriding existing toolbar provider for toolbar provider 'Recent' in bundle 'ChimeraX-Toolbar'
WARNING: Traceback (most recent call last):
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 387, in init_manager
    return api._api_caller.init_manager(api, session, self, name, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1300, in init_manager
    return cls._get_func(api, "init_manager")(session, bi, name, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/__init__.py", line 53, in init_manager
    session.alignments = AlignmentsManager(session, name, bundle_info)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/manager.py", line 46, in __init__
    super().__init__(name)
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 994, in __init__
    ts._init_single_manager(self)
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 873, in _init_single_manager
    mgr.add_provider(pbi, pvdr, **kw)
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/manager.py", line 100, in add_provider
    raise ValueError("Viewer subcommand name '%s' is already taken" % subcommand_name)
ValueError: Viewer subcommand name 'viewer' is already taken

WARNING: Replacing opener for 'IMOD model' from IMOD bundle with that from IMOD bundle
WARNING: Replacing opener for 'EMDB SFF' from EMDB-SFF bundle with that from EMDB-SFF bundle
WARNING: Replacing opener for 'VIPERdb' from VIPERdb bundle with that from VIPERdb bundle
WARNING: Replacing opener for 'Wavefront OBJ' from WavefrontOBJ bundle with that from WavefrontOBJ bundle
WARNING: Replacing fetcher for 'iupac' and format IUPAC from IUPAC bundle with that from IUPAC bundle
WARNING: Replacing opener for 'Model Positions' from Positions bundle with that from Positions bundle
WARNING: Replacing opener for 'Pseudobonds' from ReadPbonds bundle with that from ReadPbonds bundle
WARNING: Replacing opener for 'NRRD Medical Imaging' from NRRD bundle with that from NRRD bundle
WARNING: Replacing opener for 'define attribute' from StdCommands bundle with that from StdCommands bundle
WARNING: Replacing opener for 'Schrodinger Maestro' from Maestro bundle with that from Maestro bundle
WARNING: Replacing fetcher for 'uniprot' and format UniProt sequence from uniprot bundle with that from uniprot bundle
WARNING: Replacing opener for 'Deep mutational scan' from DeepMutationalScan bundle with that from DeepMutationalScan bundle
WARNING: Replacing opener for 'Amira mesh' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'APBS potential' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'BRIX density map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'CCP4 density map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'Chimera map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'CNS or XPLOR density map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'DelPhi or GRASP potential' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'DeltaVision map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'DSN6 density map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'DOCK scoring grid' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'EMAN HDF map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'Gaussian cube grid' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'gOpenMol grid' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'HDF map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'Image stack' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'IMAGIC density map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'Imaris map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'IMOD map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'MacMolPlt grid' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'MRC density map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'NetCDF map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'Priism microscope image' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'PROFEC free energy grid' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'Purdue image format' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'SITUS map file' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'SPIDER volume data' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'TOM toolbox EM density map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'UHBD grid, binary' from Map bundle with that from Map bundle
WARNING: Replacing fetcher for 'eds' and format CCP4 density map from Map bundle with that from Map bundle
WARNING: Replacing fetcher for 'edsdiff' and format CCP4 density map from Map bundle with that from Map bundle
WARNING: Replacing fetcher for 'emdb' and format CCP4 density map from Map bundle with that from Map bundle
WARNING: Replacing fetcher for 'emdb_europe' and format CCP4 density map from Map bundle with that from Map bundle
WARNING: Replacing fetcher for 'emdb_us' and format CCP4 density map from Map bundle with that from Map bundle
WARNING: Replacing fetcher for 'emdb_japan' and format CCP4 density map from Map bundle with that from Map bundle
WARNING: Replacing fetcher for 'emdb_china' and format CCP4 density map from Map bundle with that from Map bundle
WARNING: Replacing fetcher for 'emdb_fits' and format CCP4 density map from Map bundle with that from Map bundle
WARNING: Replacing fetcher for 'redo' and format MTZ from Map bundle with that from Map bundle
WARNING: Replacing opener for 'STORM microscopy' from Storm bundle with that from Storm bundle
WARNING: Replacing fetcher for 'help' and format HTML from Help bundle with that from Help bundle
WARNING: Replacing fetcher for 'http' and format HTML from Help bundle with that from Help bundle
WARNING: Replacing fetcher for 'https' and format HTML from Help bundle with that from Help bundle
WARNING: Replacing opener for 'HTML' from Help bundle with that from Help bundle
WARNING: Replacing fetcher for 'pubchem' and format sdf from PubChem bundle with that from PubChem bundle
WARNING: Replacing opener for 'PDB' from PDB bundle with that from PDB bundle
WARNING: Replacing fetcher for 'pdb' and format pdb from PDB bundle with that from PDB bundle
WARNING: Replacing fetcher for 'pdbe' and format pdb from PDB bundle with that from PDB bundle
WARNING: Replacing fetcher for 'pdbj' and format pdb from PDB bundle with that from PDB bundle
WARNING: Replacing fetcher for 'redo' and format pdb from PDB bundle with that from PDB bundle
WARNING: Replacing fetcher for 'cellpack' and format cellpack from CellPack bundle with that from CellPack bundle
WARNING: Replacing opener for 'ChimeraX session' from CoreFormats bundle with that from CoreFormats bundle
WARNING: Replacing opener for 'ChimeraX commands' from CoreFormats bundle with that from CoreFormats bundle
WARNING: Replacing opener for 'Python' from CoreFormats bundle with that from CoreFormats bundle
WARNING: Replacing opener for 'Compiled Python' from CoreFormats bundle with that from CoreFormats bundle
WARNING: Replacing fetcher for 'http' and format web fetch from CoreFormats bundle with that from CoreFormats bundle
WARNING: Replacing fetcher for 'https' and format web fetch from CoreFormats bundle with that from CoreFormats bundle
WARNING: Replacing fetcher for 'ftp' and format web fetch from CoreFormats bundle with that from CoreFormats bundle
WARNING: Replacing opener for 'NIfTI Medical Imaging' from Nifti bundle with that from Nifti bundle
WARNING: Replacing fetcher for 'tcia' and format NIfTI Medical Imaging from Nifti bundle with that from Nifti bundle
WARNING: Replacing opener for 'Gromacs full-precision coordinates' from MDcrds bundle with that from MDcrds bundle
WARNING: Replacing opener for 'Gromacs compressed coordinates' from MDcrds bundle with that from MDcrds bundle
WARNING: Replacing opener for 'DCD coordinates' from MDcrds bundle with that from MDcrds bundle
WARNING: Replacing opener for 'Amber netCDF coordinates' from MDcrds bundle with that from MDcrds bundle
WARNING: Replacing opener for 'Gromos87 coordinates' from MDcrds bundle with that from MDcrds bundle
WARNING: Replacing opener for 'Protein structure file' from MDcrds bundle with that from MDcrds bundle
WARNING: Replacing opener for 'AlphaFold PAE' from AlphaFold bundle with that from AlphaFold bundle
WARNING: Replacing fetcher for 'alphafold' and format mmCIF from AlphaFold bundle with that from AlphaFold bundle
WARNING: Replacing fetcher for 'alphafold_pae' and format pae from AlphaFold bundle with that from AlphaFold bundle
WARNING: Replacing opener for 'Macromolecular Transmission' from MMTF bundle with that from MMTF bundle
WARNING: Replacing fetcher for 'pdb' and format mmtf from MMTF bundle with that from MMTF bundle
WARNING: Replacing opener for 'Marker model' from Markers bundle with that from Markers bundle
WARNING: Replacing opener for 'NMRSTAR' from NMRSTAR bundle with that from NMRSTAR bundle
WARNING: Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle
WARNING: Replacing opener for 'GL Transmission' from gltf bundle with that from gltf bundle
WARNING: Replacing opener for 'AutoDock PDBQT' from ViewDockX bundle with that from ViewDockX bundle
WARNING: Replacing opener for 'Sybyl Mol2' from ViewDockX bundle with that from ViewDockX bundle
WARNING: Replacing opener for 'ZDOCK' from ViewDockX bundle with that from ViewDockX bundle
WARNING: Replacing opener for 'SwissDock' from ViewDockX bundle with that from ViewDockX bundle
WARNING: Replacing opener for 'photo' from ImageFormats bundle with that from ImageFormats bundle
WARNING: Replacing opener for 'Stereolithography' from STL bundle with that from STL bundle
WARNING: Replacing opener for 'SWC neurons' from Neuron bundle with that from Neuron bundle
WARNING: Replacing opener for 'MDL MOL/SDF' from SDF bundle with that from SDF bundle
WARNING: Replacing opener for 'Segmentation' from Segger bundle with that from Segger bundle
WARNING: Replacing opener for 'COLLADA' from Surface bundle with that from Surface bundle
WARNING: Replacing opener for 'Mole' from Mole bundle with that from Mole bundle
WARNING: Replacing opener for 'DICOM medical imaging' from Dicom bundle with that from Dicom bundle
WARNING: Replacing fetcher for 'tcia' and format DICOM medical imaging from Dicom bundle with that from Dicom bundle
WARNING: Replacing opener for 'UCSF Chimera BILD' from BILD bundle with that from BILD bundle
WARNING: Replacing fetcher for 'pdbe_bio' and format mmcif from PDBBio bundle with that from PDBBio bundle
WARNING: Replacing fetcher for 'rcsb_bio' and format mmcif from PDBBio bundle with that from PDBBio bundle
WARNING: Replacing opener for 'VTK PolyData' from VTK bundle with that from VTK bundle
WARNING: Replacing opener for 'mmCIF' from mmCIF bundle with that from mmCIF bundle
WARNING: Replacing fetcher for 'pdb' and format mmcif from mmCIF bundle with that from mmCIF bundle
WARNING: Replacing fetcher for 'pdbe' and format mmcif from mmCIF bundle with that from mmCIF bundle
WARNING: Replacing fetcher for 'pdbj' and format mmcif from mmCIF bundle with that from mmCIF bundle
WARNING: Replacing fetcher for 'ccd' and format Chemical Component Dictionary from mmCIF bundle with that from mmCIF bundle
WARNING: Replacing opener for 'Small Molecule CIF' from mmCIF bundle with that from mmCIF bundle
WARNING: Replacing fetcher for 'cod' and format Crystallography Open Database from mmCIF bundle with that from mmCIF bundle
WARNING: Replacing fetcher for 'pcod' and format Predicted Crystallography Open Database from mmCIF bundle with that from mmCIF bundle
WARNING: Replacing fetcher for 'redo' and format mmcif from mmCIF bundle with that from mmCIF bundle
WARNING: Replacing opener for 'Clustal ALN' from Alignments bundle with that from Alignments bundle
WARNING: Replacing opener for 'FASTA' from Alignments bundle with that from Alignments bundle
WARNING: Replacing opener for 'HSSP' from Alignments bundle with that from Alignments bundle
WARNING: Replacing opener for 'GCG Multiple Sequence File' from Alignments bundle with that from Alignments bundle
WARNING: Replacing opener for 'Pfam' from Alignments bundle with that from Alignments bundle
WARNING: Replacing opener for 'NBRF/PIR' from Alignments bundle with that from Alignments bundle
WARNING: Replacing opener for 'GCG Rich Sequence' from Alignments bundle with that from Alignments bundle
WARNING: Replacing opener for 'Stockholm' from Alignments bundle with that from Alignments bundle
WARNING: Replacing opener for 'Integrative/Hybrid Models' from IHM bundle with that from IHM bundle
WARNING: Replacing fetcher for 'pdbdev' and format Integrative/Hybrid Models from IHM bundle with that from IHM bundle
WARNING: Replacing fetcher for 'esmfold' and format PDB from ESMFold bundle with that from ESMFold bundle
WARNING: Replacing fetcher for 'smiles' and format SMILES from Smiles bundle with that from Smiles bundle
WARNING: Replacing opener for 'Directional FSC' from ColorGlobe bundle with that from ColorGlobe bundle
WARNING: Replacing opener for 'IMOD model' from IMOD bundle with that from IMOD bundle
WARNING: Replacing opener for 'EMDB SFF' from EMDB-SFF bundle with that from EMDB-SFF bundle
WARNING: Replacing opener for 'VIPERdb' from VIPERdb bundle with that from VIPERdb bundle
WARNING: Replacing opener for 'Wavefront OBJ' from WavefrontOBJ bundle with that from WavefrontOBJ bundle
WARNING: Replacing fetcher for 'iupac' and format IUPAC from IUPAC bundle with that from IUPAC bundle
WARNING: Replacing opener for 'Model Positions' from Positions bundle with that from Positions bundle
WARNING: Replacing opener for 'Pseudobonds' from ReadPbonds bundle with that from ReadPbonds bundle
WARNING: Replacing opener for 'NRRD Medical Imaging' from NRRD bundle with that from NRRD bundle
WARNING: Replacing opener for 'define attribute' from StdCommands bundle with that from StdCommands bundle
WARNING: Replacing opener for 'Schrodinger Maestro' from Maestro bundle with that from Maestro bundle
WARNING: Replacing fetcher for 'uniprot' and format UniProt sequence from uniprot bundle with that from uniprot bundle
WARNING: Replacing opener for 'Deep mutational scan' from DeepMutationalScan bundle with that from DeepMutationalScan bundle
WARNING: Replacing opener for 'Amira mesh' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'APBS potential' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'BRIX density map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'CCP4 density map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'Chimera map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'CNS or XPLOR density map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'DelPhi or GRASP potential' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'DeltaVision map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'DSN6 density map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'DOCK scoring grid' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'EMAN HDF map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'Gaussian cube grid' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'gOpenMol grid' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'HDF map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'Image stack' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'IMAGIC density map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'Imaris map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'IMOD map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'MacMolPlt grid' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'MRC density map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'NetCDF map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'Priism microscope image' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'PROFEC free energy grid' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'Purdue image format' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'SITUS map file' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'SPIDER volume data' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'TOM toolbox EM density map' from Map bundle with that from Map bundle
WARNING: Replacing opener for 'UHBD grid, binary' from Map bundle with that from Map bundle
WARNING: Replacing fetcher for 'eds' and format CCP4 density map from Map bundle with that from Map bundle
WARNING: Replacing fetcher for 'edsdiff' and format CCP4 density map from Map bundle with that from Map bundle
WARNING: Replacing fetcher for 'emdb' and format CCP4 density map from Map bundle with that from Map bundle
WARNING: Replacing fetcher for 'emdb_europe' and format CCP4 density map from Map bundle with that from Map bundle
WARNING: Replacing fetcher for 'emdb_us' and format CCP4 density map from Map bundle with that from Map bundle
WARNING: Replacing fetcher for 'emdb_japan' and format CCP4 density map from Map bundle with that from Map bundle
WARNING: Replacing fetcher for 'emdb_china' and format CCP4 density map from Map bundle with that from Map bundle
WARNING: Replacing fetcher for 'emdb_fits' and format CCP4 density map from Map bundle with that from Map bundle
WARNING: Replacing fetcher for 'redo' and format MTZ from Map bundle with that from Map bundle
WARNING: Replacing opener for 'STORM microscopy' from Storm bundle with that from Storm bundle
WARNING: Replacing fetcher for 'help' and format HTML from Help bundle with that from Help bundle
WARNING: Replacing fetcher for 'http' and format HTML from Help bundle with that from Help bundle
WARNING: Replacing fetcher for 'https' and format HTML from Help bundle with that from Help bundle
WARNING: Replacing opener for 'HTML' from Help bundle with that from Help bundle
WARNING: Replacing fetcher for 'pubchem' and format sdf from PubChem bundle with that from PubChem bundle
WARNING: Replacing opener for 'PDB' from PDB bundle with that from PDB bundle
WARNING: Replacing fetcher for 'pdb' and format pdb from PDB bundle with that from PDB bundle
WARNING: Replacing fetcher for 'pdbe' and format pdb from PDB bundle with that from PDB bundle
WARNING: Replacing fetcher for 'pdbj' and format pdb from PDB bundle with that from PDB bundle
WARNING: Replacing fetcher for 'redo' and format pdb from PDB bundle with that from PDB bundle
WARNING: Replacing fetcher for 'cellpack' and format cellpack from CellPack bundle with that from CellPack bundle
WARNING: Replacing opener for 'ChimeraX session' from CoreFormats bundle with that from CoreFormats bundle
WARNING: Replacing opener for 'ChimeraX commands' from CoreFormats bundle with that from CoreFormats bundle
WARNING: Replacing opener for 'Python' from CoreFormats bundle with that from CoreFormats bundle
WARNING: Replacing opener for 'Compiled Python' from CoreFormats bundle with that from CoreFormats bundle
WARNING: Replacing fetcher for 'http' and format web fetch from CoreFormats bundle with that from CoreFormats bundle
WARNING: Replacing fetcher for 'https' and format web fetch from CoreFormats bundle with that from CoreFormats bundle
WARNING: Replacing fetcher for 'ftp' and format web fetch from CoreFormats bundle with that from CoreFormats bundle
WARNING: Replacing opener for 'NIfTI Medical Imaging' from Nifti bundle with that from Nifti bundle
WARNING: Replacing fetcher for 'tcia' and format NIfTI Medical Imaging from Nifti bundle with that from Nifti bundle
WARNING: Replacing opener for 'Gromacs full-precision coordinates' from MDcrds bundle with that from MDcrds bundle
WARNING: Replacing opener for 'Gromacs compressed coordinates' from MDcrds bundle with that from MDcrds bundle
WARNING: Replacing opener for 'DCD coordinates' from MDcrds bundle with that from MDcrds bundle
WARNING: Replacing opener for 'Amber netCDF coordinates' from MDcrds bundle with that from MDcrds bundle
WARNING: Replacing opener for 'Gromos87 coordinates' from MDcrds bundle with that from MDcrds bundle
WARNING: Replacing opener for 'Protein structure file' from MDcrds bundle with that from MDcrds bundle
WARNING: Replacing opener for 'AlphaFold PAE' from AlphaFold bundle with that from AlphaFold bundle
WARNING: Replacing fetcher for 'alphafold' and format mmCIF from AlphaFold bundle with that from AlphaFold bundle
WARNING: Replacing fetcher for 'alphafold_pae' and format pae from AlphaFold bundle with that from AlphaFold bundle
WARNING: Replacing opener for 'Macromolecular Transmission' from MMTF bundle with that from MMTF bundle
WARNING: Replacing fetcher for 'pdb' and format mmtf from MMTF bundle with that from MMTF bundle
WARNING: Replacing opener for 'Marker model' from Markers bundle with that from Markers bundle
WARNING: Replacing opener for 'NMRSTAR' from NMRSTAR bundle with that from NMRSTAR bundle
WARNING: Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle
WARNING: Replacing opener for 'GL Transmission' from gltf bundle with that from gltf bundle
WARNING: Replacing opener for 'AutoDock PDBQT' from ViewDockX bundle with that from ViewDockX bundle
WARNING: Replacing opener for 'Sybyl Mol2' from ViewDockX bundle with that from ViewDockX bundle
WARNING: Replacing opener for 'ZDOCK' from ViewDockX bundle with that from ViewDockX bundle
WARNING: Replacing opener for 'SwissDock' from ViewDockX bundle with that from ViewDockX bundle
WARNING: Replacing opener for 'photo' from ImageFormats bundle with that from ImageFormats bundle
WARNING: Replacing opener for 'Stereolithography' from STL bundle with that from STL bundle
WARNING: Replacing opener for 'SWC neurons' from Neuron bundle with that from Neuron bundle
WARNING: Replacing opener for 'MDL MOL/SDF' from SDF bundle with that from SDF bundle
WARNING: Replacing opener for 'Segmentation' from Segger bundle with that from Segger bundle
WARNING: Replacing opener for 'COLLADA' from Surface bundle with that from Surface bundle
WARNING: Replacing opener for 'Mole' from Mole bundle with that from Mole bundle
WARNING: Replacing opener for 'DICOM medical imaging' from Dicom bundle with that from Dicom bundle
WARNING: Replacing fetcher for 'tcia' and format DICOM medical imaging from Dicom bundle with that from Dicom bundle
WARNING: Replacing opener for 'UCSF Chimera BILD' from BILD bundle with that from BILD bundle
WARNING: Replacing fetcher for 'pdbe_bio' and format mmcif from PDBBio bundle with that from PDBBio bundle
WARNING: Replacing fetcher for 'rcsb_bio' and format mmcif from PDBBio bundle with that from PDBBio bundle
WARNING: Replacing opener for 'VTK PolyData' from VTK bundle with that from VTK bundle
WARNING: Replacing opener for 'mmCIF' from mmCIF bundle with that from mmCIF bundle
WARNING: Replacing fetcher for 'pdb' and format mmcif from mmCIF bundle with that from mmCIF bundle
WARNING: Replacing fetcher for 'pdbe' and format mmcif from mmCIF bundle with that from mmCIF bundle
WARNING: Replacing fetcher for 'pdbj' and format mmcif from mmCIF bundle with that from mmCIF bundle
WARNING: Replacing fetcher for 'ccd' and format Chemical Component Dictionary from mmCIF bundle with that from mmCIF bundle
WARNING: Replacing opener for 'Small Molecule CIF' from mmCIF bundle with that from mmCIF bundle
WARNING: Replacing fetcher for 'cod' and format Crystallography Open Database from mmCIF bundle with that from mmCIF bundle
WARNING: Replacing fetcher for 'pcod' and format Predicted Crystallography Open Database from mmCIF bundle with that from mmCIF bundle
WARNING: Replacing fetcher for 'redo' and format mmcif from mmCIF bundle with that from mmCIF bundle
WARNING: Replacing opener for 'Clustal ALN' from Alignments bundle with that from Alignments bundle
WARNING: Replacing opener for 'FASTA' from Alignments bundle with that from Alignments bundle
WARNING: Replacing opener for 'HSSP' from Alignments bundle with that from Alignments bundle
WARNING: Replacing opener for 'GCG Multiple Sequence File' from Alignments bundle with that from Alignments bundle
WARNING: Replacing opener for 'Pfam' from Alignments bundle with that from Alignments bundle
WARNING: Replacing opener for 'NBRF/PIR' from Alignments bundle with that from Alignments bundle
WARNING: Replacing opener for 'GCG Rich Sequence' from Alignments bundle with that from Alignments bundle
WARNING: Replacing opener for 'Stockholm' from Alignments bundle with that from Alignments bundle
WARNING: Replacing opener for 'Integrative/Hybrid Models' from IHM bundle with that from IHM bundle
WARNING: Replacing fetcher for 'pdbdev' and format Integrative/Hybrid Models from IHM bundle with that from IHM bundle
WARNING: Replacing fetcher for 'esmfold' and format PDB from ESMFold bundle with that from ESMFold bundle
WARNING: Replacing fetcher for 'smiles' and format SMILES from Smiles bundle with that from Smiles bundle
WARNING: Replacing opener for 'Directional FSC' from ColorGlobe bundle with that from ColorGlobe bundle
WARNING: Replacing file-saver for 'VRML' from vrml bundle with that from vrml bundle
WARNING: Replacing file-saver for 'Wavefront OBJ' from WavefrontOBJ bundle with that from WavefrontOBJ bundle
WARNING: Replacing file-saver for 'Model Positions' from Positions bundle with that from Positions bundle
WARNING: Replacing file-saver for 'Pseudobonds' from ReadPbonds bundle with that from ReadPbonds bundle
WARNING: Replacing file-saver for 'NRRD Medical Imaging' from NRRD bundle with that from NRRD bundle
WARNING: Replacing file-saver for 'define attribute' from StdCommands bundle with that from StdCommands bundle
WARNING: Replacing file-saver for 'BRIX density map' from Map bundle with that from Map bundle
WARNING: Replacing file-saver for 'CCP4 density map' from Map bundle with that from Map bundle
WARNING: Replacing file-saver for 'Chimera map' from Map bundle with that from Map bundle
WARNING: Replacing file-saver for 'ImageJ TIFF map' from Map bundle with that from Map bundle
WARNING: Replacing file-saver for 'IMAGIC density map' from Map bundle with that from Map bundle
WARNING: Replacing file-saver for 'MRC density map' from Map bundle with that from Map bundle
WARNING: Replacing file-saver for 'PDB' from PDB bundle with that from PDB bundle
WARNING: Replacing file-saver for 'ChimeraX session' from CoreFormats bundle with that from CoreFormats bundle
WARNING: Replacing file-saver for 'X3D' from CoreFormats bundle with that from CoreFormats bundle
WARNING: Replacing file-saver for 'NIfTI Medical Imaging' from Nifti bundle with that from Nifti bundle
WARNING: Replacing file-saver for 'DCD coordinates' from MDcrds bundle with that from MDcrds bundle
WARNING: Replacing file-saver for 'Sybyl Mol2' from Mol2 bundle with that from Mol2 bundle
WARNING: Replacing file-saver for 'Marker model' from Markers bundle with that from Markers bundle
WARNING: Replacing file-saver for 'GL Transmission' from gltf bundle with that from gltf bundle
WARNING: Replacing file-saver for 'Bitmap image' from ImageFormats bundle with that from ImageFormats bundle
WARNING: Replacing file-saver for 'Graphics Interchange Format' from ImageFormats bundle with that from ImageFormats bundle
WARNING: Replacing file-saver for 'Joint Photographic Experts Group image' from ImageFormats bundle with that from ImageFormats bundle
WARNING: Replacing file-saver for 'Portable Network Graphics' from ImageFormats bundle with that from ImageFormats bundle
WARNING: Replacing file-saver for 'Portable Pixmap format' from ImageFormats bundle with that from ImageFormats bundle
WARNING: Replacing file-saver for 'Tagged Image File format' from ImageFormats bundle with that from ImageFormats bundle
WARNING: Replacing file-saver for 'Stereolithography' from STL bundle with that from STL bundle
WARNING: Replacing file-saver for 'Segmentation' from Segger bundle with that from Segger bundle
WARNING: Replacing file-saver for 'DICOM medical imaging' from Dicom bundle with that from Dicom bundle
WARNING: Replacing file-saver for 'VTK PolyData' from VTK bundle with that from VTK bundle
WARNING: Replacing file-saver for 'mmCIF' from mmCIF bundle with that from mmCIF bundle
WARNING: Replacing file-saver for 'Clustal ALN' from Alignments bundle with that from Alignments bundle
WARNING: Replacing file-saver for 'FASTA' from Alignments bundle with that from Alignments bundle
WARNING: Replacing file-saver for 'NBRF/PIR' from Alignments bundle with that from Alignments bundle
WARNING: Traceback (most recent call last):
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 387, in init_manager
    return api._api_caller.init_manager(api, session, self, name, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1300, in init_manager
    return cls._get_func(api, "init_manager")(session, bi, name, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/__init__.py", line 53, in init_manager
    session.alignments = AlignmentsManager(session, name, bundle_info)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/manager.py", line 46, in __init__
    super().__init__(name)
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 994, in __init__
    ts._init_single_manager(self)
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 873, in _init_single_manager
    mgr.add_provider(pbi, pvdr, **kw)
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/manager.py", line 100, in add_provider
    raise ValueError("Viewer subcommand name '%s' is already taken" % subcommand_name)
ValueError: Viewer subcommand name 'viewer' is already taken

NOTE: FYI: command is replacing existing command: "toolshed updates"
WARNING: Traceback (most recent call last):
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 376, in initialize
    api._api_caller.initialize(api, session, self)
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1296, in initialize
    return cls._get_func(api, "initialize")(session, bi)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/vive/__init__.py", line 32, in initialize
    session.triggers.add_trigger('vr started')
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 340, in add_trigger
    raise KeyError("Trigger '%s' already exists" % name)
KeyError: "Trigger 'vr started' already exists"

WARNING: Traceback (most recent call last):
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 376, in initialize
    api._api_caller.initialize(api, session, self)
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1296, in initialize
    return cls._get_func(api, "initialize")(session, bi)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/basic_actions/__init__.py", line 35, in initialize
    session.basic_actions = BasicActions(session)
                            ^^^^^^^^^^^^^^^^^^^^^
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/basic_actions/statemgr.py", line 44, in __init__
    t.add_trigger(DEFINE_NAMESEL)
  File "/Users/zjp/git/rbvi/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 340, in add_trigger
    raise KeyError("Trigger '%s' already exists" % name)
KeyError: "Trigger 'define named selection' already exists"

ERROR: Bundle 'ChimeraX-Alignments' custom initialization failed
ERROR: Bundle 'ChimeraX-Alignments' custom initialization failed
ERROR: Bundle 'ChimeraX-Vive' custom initialization failed
ERROR: Bundle 'ChimeraX-BasicActions' custom initialization failed
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Change History (12)

comment:1 by Zach Pearson, 16 months ago

This persists if I reinstall graphics in normal mode.

comment:2 by Eric Pettersen, 16 months ago

Component: Unassigned → Tool Shed

comment:3 by Zach Pearson, 16 months ago

Summary: Editable installs break ChimeraX → Duplicate bundles in cache

comment:4 by Zach Pearson, 16 months ago

If I delete the cache I can see in debug output that write_cache is only called once, but when we're rebuilding the cache each bundle is listed twice. This behavior seems to only occur if ChimeraX is run normally, when I run it from my debugger it gets a unique list (????)

comment:5 by Zach Pearson, 16 months ago

At least going from the debugger to the application the application complains that a different executable was used to build the cache and so it's going to rebuild it (this should be smarter but looks like a red herring).

comment:6 by Zach Pearson, 16 months ago

importlib itself is counting the packages twice for whatever reason 

Toolshed: Packages: 576
Toolshed: Packages: 330

comment:8 by Greg Couch, 16 months ago 

That looks like the issue.

When it is fixed upstream, it should be in the importlib_metadata pypi 
package, which is an advance version of the builtin importlib.metadata. 
We are using the latter.

comment:9 by Zach Pearson, 16 months ago

I'm going to do a fresh build and see if I can reproduce with no editable packages. It seems odd to me that all of them are counted twice and not just the editable one. Maybe the editable packages triggers all of them being counted twice; the issue seems to complain about just the one but it's possible. In any case maybe I can contribute.

comment:10 by Zach Pearson, 16 months ago

Just noting some more weird behavior: Couldn't reproduce until I installed blastprotein in editable mode. Things continued to work -- though ChimeraX complained that it couldn't find the tool anymore -- until I reinstalled blastprotein the normal way and all hell broke loose again. I'm going to put a workaround in toolshed/installed.py that kicks out duplicates so I can go back to other work but won't close this until it's resolved upstream.

comment:12 by Zach Pearson, 16 months ago

Milestone: 1.9
Priority: blocker → moderate

I'm demoting this to moderate and unmilestoning it. It doesn't make sense to have a milestoned ticket that will have to be resolved on another project's timeline and with the workaround it's no longer a blocker.

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