id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15492 Duplicate bundles in cache Zach Pearson Zach Pearson "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 CoreGraphics PDF has logged an error. Set environment variable ""CG_PDF_VERBOSE"" to learn more. CoreGraphics PDF has logged an error. Set environment variable ""CG_PDF_VERBOSE"" to learn more. }}}" defect assigned moderate Tool Shed Greg Couch all ChimeraX