chimerax --debug NOTE: Initializing core Toolshed: __init__ False False None Toolshed: cache dir: /home/jobilinux/.cache/ChimeraX/1.9/toolshed Toolshed: site dir: /home/jobilinux/.local/share/ChimeraX/1.9/lib/python3.11/site-packages Toolshed: loading bundles available bundle cache has not been initialized yet Toolshed: reload False False Toolshed: _bundle_cache False Toolshed: InstalledBundleCache.load: rebuild_cache False Toolshed: InstalledBundleCache._read_cache: /home/jobilinux/.cache/ChimeraX/1.9/toolshed/bundle_info.cache Toolshed: _is_cache_newer Toolshed: InstalledBundleCache.load: rebuilding cache Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-RestServer (installed) [version: 1.3.1] [api package: chimerax.rest_server] [category: General] [command: remotecontrol rest [categories: General] [synopsis: Control REST server]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-TaskManager (installed) [version: 1.0] [api package: chimerax.taskmanager] [category: User Interface] [tool: Task Manager [categories: Utilities] [synopsis: Visualize open tasks]] [command: taskman [categories: Utilities] [synopsis: Visualize open tasks]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Atomic (installed) [version: 1.58.8] [api package: chimerax.atomic] [category: Structure Analysis, Structure Editing] [command: log chains [categories: General] [synopsis: show chain info in log]] [command: combine [categories: Structure Editing] [synopsis: copy or combine structure models]] [command: pbond [categories: Structure Editing] [synopsis: create a pseudobond]] [command: ~pbond [categories: Structure Analysis] [synopsis: delete a pseudobond]] [command: label missing [categories: Structure Analysis] [synopsis: label missing-structure pseudobonds]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-AddCharge (installed) [version: 1.5.18] [api package: chimerax.add_charge] [category: Structure Editing] [tool: Add Charges [categories: Structure Editing] [synopsis: Add partial charges to structure]] [command: addcharge [categories: Structure Editing] [synopsis: Add charges]] [command: addcharge nonstd [categories: Structure Editing] [synopsis: Add charges to non-standard residues]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Log (installed) [version: 1.2] [api package: chimerax.log] [category: General] [tool: Log [categories: General] [synopsis: Log of information and output]] [command: echo [categories: General] [synopsis: Log a line of text]] [command: log [categories: General] [synopsis: manipulate the Log tool]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-AlignmentHdrs (installed) [version: 3.5] [api package: chimerax.alignment_headers] [category: Sequence] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-CheckWaters (installed) [version: 1.4] [api package: chimerax.check_waters] [category: Volume Data] [tool: Check Waters [categories: Structure Analysis] [synopsis: Check water placement in a map]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Modeller (installed) [version: 1.5.18] [api package: chimerax.modeller] [category: Sequence, Structure Prediction] [tool: Modeller Comparative [categories: Sequence, Structure Prediction] [synopsis: Generate comparative models]] [tool: Model Loops [categories: Sequence, Structure Prediction] [synopsis: Model/remodel structure segments]] [command: modeller comparative [categories: Sequence, Structure Prediction] [synopsis: Generate comparative models]] [command: modeller loops [categories: Sequence, Structure Prediction] [synopsis: Fill missing structure]] [command: modeller refine [categories: Sequence, Structure Prediction] [synopsis: Fill missing structure]] [command: modeller scores [categories: Sequence, Structure Prediction] [synopsis: Fetch Modeller scores for a model]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-MapFilter (installed) [version: 2.0.1] [api package: chimerax.map_filter] [category: Volume Data] [tool: Map Filter [categories: Volume Data] [synopsis: Apply filters to maps]] [command: volume add [categories: Volume data] [synopsis: Add two or more maps]] [command: volume bin [categories: Volume data] [synopsis: Average map values over bins to reduce map size]] [command: volume boxes [categories: Volume data] [synopsis: Extract maps for boxes around selected atoms]] [command: volume copy [categories: Volume data] [synopsis: Copy a map or a map subregion]] [command: volume cover [categories: Volume data] [synopsis: Use symmetry to extend a map to cover a region]] [command: volume falloff [categories: Volume data] [synopsis: Smooth map values where map falls to zero]] [command: volume flatten [categories: Volume data] [synopsis: Flatten map gradients]] [command: volume flip [categories: Volume data] [synopsis: Reverse axis directions]] [command: volume fourier [categories: Volume data] [synopsis: Fourier transform a map]] [command: volume gaussian [categories: Volume data] [synopsis: Convolve map with a Gaussian for smoothing]] [command: volume laplacian [categories: Volume data] [synopsis: Laplace filter a map to enhance edges]] [command: volume localCorrelation [categories: Volume data] [synopsis: Compute correlation between maps over a slid]] [command: volume maximum [categories: Volume data] [synopsis: Maximum pointwise values of 2 or more maps]] [command: volume minimum [categories: Volume data] [synopsis: Minimum pointwise values of 2 or more maps]] [command: volume median [categories: Volume data] [synopsis: Median map value over a sliding window]] [command: volume morph [categories: Volume data] [synopsis: Linearly interpolate maps]] [command: volume multiply [categories: Volume data] [synopsis: Multiply maps pointwise]] [command: volume new [categories: Volume data] [synopsis: Create a new map with zero values]] [command: volume octant [categories: Volume data] [synopsis: Zero all but an octant of a map]] [command: volume ~octant [categories: Volume data] [synopsis: Zero an octant of a map]] [command: volume permuteAxes [categories: Volume data] [synopsis: Permute map axes]] [command: volume resample [categories: Volume data] [synopsis: Resample a map on the grid of another map]] [command: volume ridges [categories: Volume data] [synopsis: Filter to detect map ridges]] [command: volume scale [categories: Volume data] [synopsis: Scale and shift map values]] [command: volume sharpen [categories: Volume data] [synopsis: Sharpen map by amplifying high-frequencies using bfactor]] [command: volume subtract [categories: Volume data] [synopsis: Subtract maps pointwise]] [command: volume threshold [categories: Volume data] [synopsis: Set map values below a threshold to zero]] [command: volume tile [categories: Volume data] [synopsis: Create a single plane map by tiling planes of a map]] [command: volume unbend [categories: Volume data] [synopsis: Unwarp a map along a curved rectangular tube]] [command: volume unroll [categories: Volume data] [synopsis: Unroll a cylindrical shell to form a new map]] [command: volume zone [categories: Volume data] [synopsis: Zero map values beyond a distance range from atoms]] [command: volume unzone [categories: Volume data] [synopsis: Show full map with no surface masking]] [command: vop [categories: Volume data] [synopsis: Synonym for volume command for backward compatibility with Chimera]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-FunctionKey (installed) [version: 1.0.1] [api package: chimerax.function_key] [category: General] [command: ui functionkey [categories: General] [synopsis: Assign function keys to run commands]] [command: functionkey [categories: General] [synopsis: Assign function keys to run commands]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-ChangeChains (installed) [version: 1.1] [api package: chimerax.change_chains] [category: Structure Editing] [tool: Change Chain IDs [categories: Structure Editing] [synopsis: change chain IDs]] [command: changechains [categories: Structure Editing] [synopsis: change chain IDs]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-IUPAC (installed) [version: 1.0] [api package: chimerax.iupac] [category: Molecular structure] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Dssp (installed) [version: 2.0] [api package: chimerax.dssp] [category: Structure Analysis] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-SwapAA (installed) [version: 2.0.1] [api package: chimerax.swapaa] [category: Structure Editing] [command: swapaa mousemode [categories: Replace an amino acid] [synopsis: Replaces amino acid with a specified standard amino acid]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-vrml (installed) [version: 1.0] [api package: chimerax.vrml] [category: Generic 3D objects] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-VolumeMenu (installed) [version: 1.0.1] [api package: chimerax.volume_menu] [category: Volume data] [tool: Show Volume Menu [categories: Volume Data] [synopsis: Add a top level volume menu]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-AxesPlanes (installed) [version: 2.4] [api package: chimerax.axes_planes] [category: Structure Analysis] [command: define plane [categories: Structure Analysis] [synopsis: Create a plane in the scene]] [command: define axis [categories: Structure Analysis] [synopsis: Create an axis in the scene]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Segment (installed) [version: 1.0.1] [api package: chimerax.segment] [category: Volume data] [command: segmentation [categories: Volume data] [synopsis: color and surface segmentations]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-gltf (installed) [version: 1.0] [api package: chimerax.gltf] [category: Generic 3D objects] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-SimilarStructures (installed) [version: 1.0.1] [api package: chimerax.similarstructures] [category: Structure Comparison] [tool: Similar Structures [categories: Structure Analysis] [synopsis: Search PDB or AlphaFold databases for protein structures with similar fold or sequence to a specified structure]] [tool: Foldseek [categories: Structure Analysis] [synopsis: Search PDB or AlphaFold databases for protein structures matching the fold of a specified structure]] [command: foldseek [categories: Structure Comparison] [synopsis: Search PDB or AlphaFold databases for protein structures matching the fold of a specified structure]] [command: similarstructures open [categories: Structure Comparison] [synopsis: Open and align a hit from a similar structure search]] [command: similarstructures close [categories: Structure Comparison] [synopsis: Close a table of similar structures]] [command: similarstructures list [categories: Structure Comparison] [synopsis: List the names of open sets of similar structures]] [command: similarstructures sequences [categories: Structure Comparison] [synopsis: Show an image of all aligned sequences from a similar structure search, one sequence per image row]] [command: similarstructures traces [categories: Structure Comparison] [synopsis: Show backbone traces of similar structure hits aligned to query structure]] [command: similarstructures cluster [categories: Structure Comparison] [synopsis: Show plot of similar structure backbone conformation clusters]] [command: similarstructures ligands [categories: Structure Comparison] [synopsis: Create model of similar structure ligands aligned to query structure]] [command: similarstructures scrollto [categories: Structure Comparison] [synopsis: Show table row for a similar structure hit]] [command: similarstructures pairing [categories: Structure Comparison] [synopsis: Show pseudobonds between paired similar structure hit and query residues]] [command: similarstructures seqalign [categories: Structure Comparison] [synopsis: Show sequence alignement for one similar structure hit]] [command: similarstructures fetchcoords [categories: Structure Comparison] [synopsis: Fetch C-alpha coordinates of similar structure hits for clustering and showing backbone traces]] [command: sequence search [categories: Sequence] [synopsis: Search for similar sequences using MMseqs2 at PDB]] [command: similarstructures blast [categories: Sequence] [synopsis: Search for similar sequences using BLAST]] [command: similarstructures fromblast [categories: Structure Comparison] [synopsis: Convert blast results to a similar structures table]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-ModelArchive (installed) [version: 1.0] [api package: chimerax.model_archive] [category: Structure Analysis] [command: modelcif pae [categories: Structure Analysis] [synopsis: Show predicted aligned error plots for ModelCIF structures]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Nifti (installed) [version: 1.2] [api package: chimerax.nifti] [category: Volume Data] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-MMTF (installed) [version: 2.2] [api package: chimerax.mmtf] [category: Molecular structure] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-ListInfo (installed) [version: 1.2.2] [api package: chimerax.list_info] [category: General] [command: info [categories: General] [synopsis: Report attributes for models and atomic data]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-ModelSeries (installed) [version: 1.0.1] [api package: chimerax.model_series] [category: General] [command: mseries [categories: General] [synopsis: Display sequence of models one by one]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-DataFormats (installed) [version: 1.2.3] [api package: chimerax.data_formats] [category: Utilities] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Storm (installed) [version: 1.0] [api package: chimerax.storm] [category: Generic 3D object] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Topography (installed) [version: 1.0] [api package: chimerax.topography] [category: Volume Data] [command: topography [categories: Volume Data] [synopsis: Show topographic surface]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-SelInspector (installed) [version: 1.0] [api package: chimerax.sel_inspector] [category: General Controls] [tool: Selection Inspector [categories: General] [synopsis: inspect selection contents]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Mol2 (installed) [version: 2.0.3] [api package: chimerax.mol2] [category: I/O] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-VIPERdb (installed) [version: 1.0] [api package: chimerax.viperdb] [category: Structure Analysis] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Mole (installed) [version: 1.0] [api package: chimerax.mole] [category: Structure Analysis] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Help (installed) [version: 1.3] [api package: chimerax.help_viewer] [category: Documentation] [command: help [categories: Documentation] [synopsis: Display ChimeraX help]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-BuildStructure (installed) [version: 2.13.1] [api package: chimerax.build_structure] [category: Structure Analysis] [tool: Build Structure [categories: Structure Editing] [synopsis: Create/modify structures]] [command: build [categories: Structure Analysis] [synopsis: Create/modify structures]] [command: bond [categories: Structure Analysis] [synopsis: Create bond(s)]] [command: ~bond [categories: Structure Analysis] [synopsis: Remove bond(s)]] [command: bond length [categories: Structure Analysis] [synopsis: change bond length(s)]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-MedicalToolbar (installed) [version: 1.1] [api package: chimerax.medical_toolbar] [category: Toolbar] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Geometry (installed) [version: 1.3] [api package: chimerax.geometry] [category: Utility] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Alignments (installed) [version: 2.16.1] [api package: chimerax.seqalign] [category: Sequence] [command: sequence [categories: Sequence alignment] [synopsis: control/open sequence alignments]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Segmentations (installed) [version: 3.5.6] [api package: chimerax.segmentations] [category: Volume Data] [tool: Segmentations [categories: Volume Data] [synopsis: Interactively segment volumes]] [tool: Orthoplanes [categories: Volume Data] [synopsis: View planes of volumes in a dedicated tool]] [command: ui view [categories: General] [synopsis: See medical images in a 4-panel viewer]] [command: segmentations [categories: Volume Data] [synopsis: Create, edit, or destory segmentations]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Nucleotides (installed) [version: 2.0.3] [api package: chimerax.nucleotides] [category: General] [command: nucleotides [categories: General] [synopsis: Manipulate nucleotide representations]] [command: ~nucleotides [categories: General] [synopsis: Undo nucleotide representations]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-ColorGlobe (installed) [version: 1.0] [api package: chimerax.color_globe] [category: General] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Neuron (installed) [version: 1.0] [api package: chimerax.neuron] [category: Generic 3D objects] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Centroids (installed) [version: 1.4] [api package: chimerax.centroids] [category: Structure Analysis] [command: define centroid [categories: Structure Analysis] [synopsis: Depict centroid]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-LookingGlass (installed) [version: 1.1] [api package: chimerax.looking_glass] [category: General] [command: lookingglass [categories: General] [synopsis: Render to LookingGlass holographic display]] [command: device lookingglass [categories: General] [synopsis: Render to LookingGlass holographic display]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-BasicActions (installed) [version: 1.1.2] [api package: chimerax.basic_actions] [category: General] [tool: Basic Actions [categories: Depiction] [synopsis: show/hide atoms, ribbons and surfaces]] [command: name [categories: General] [synopsis: Define specifier name as a string]] [command: name frozen [categories: General] [synopsis: Define specifier name as atoms in current session matching a string]] [command: name delete [categories: General] [synopsis: Remove user-defined specifier name]] [command: name list [categories: General] [synopsis: List user-defined specifier names]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-MCopy (installed) [version: 1.0] [api package: chimerax.mcopy] [category: Molecular structure] [command: mcopy [categories: Molecular structure] [synopsis: Copy atomic structure display properties]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-AlignmentMatrices (installed) [version: 2.1] [api package: chimerax.sim_matrices] [category: Sequence alignment] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-ItemsInspection (installed) [version: 1.0.1] [api package: chimerax.items_inspection] [category: General Controls] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-ESMFold (installed) [version: 1.0] [api package: chimerax.esmfold] [category: Structure Prediction] [tool: ESMFold [categories: Structure Prediction] [synopsis: Fetch or calculate ESMFold structures]] [tool: ESMFold Error Plot [categories: Structure Prediction] [synopsis: Plot ESMFold predicted aligned error]] [command: esmfold contacts [categories: Structure Prediction] [synopsis: Show ESMFold contact pseudobond colored by predicted aligned error]] [command: esmfold fetch [categories: Structure Prediction] [synopsis: Fetch ESM Metagenomic Atlas models for a MGnify accession code]] [command: esmfold match [categories: Structure Prediction] [synopsis: Fetch ESM Metagenomic Atlas models matching a structure]] [command: esmfold pae [categories: Structure Prediction] [synopsis: Show ESMFold predicted aligned error as heatmap]] [command: esmfold predict [categories: Structure Prediction] [synopsis: Predict a structure using ESMFold]] [command: esmfold search [categories: Structure Prediction] [synopsis: Search ESMFold database using BLAST]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-UnitCell (installed) [version: 1.0.1] [api package: chimerax.unit_cell] [category: Higher-Order Structure] [tool: Unit Cell [categories: Higher-Order Structure] [synopsis: Show crystal unit cell]] [command: unitcell [categories: Higher-Order Structure] [synopsis: Place copies of atomic structure in crystal unit cell]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-StructMeasure (installed) [version: 1.2.1] [api package: chimerax.struct_measure] [category: Structure Analysis] [tool: Distances [categories: Structure Analysis] [synopsis: inter-atomic distances]] [tool: Angles/Torsions [categories: Structure Analysis] [synopsis: report angle/torsion values]] [tool: Axes/Planes/Centroids [categories: Structure Analysis] [synopsis: create/analyze axes/planes/centroids]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-CageBuilder (installed) [version: 1.0.1] [api package: chimerax.cage_builder] [category: Higher-Order Structure] [tool: Cage Builder [categories: Higher-Order Structure] [synopsis: Build polygonal meshes]] [command: cage [categories: Higher-Order Structure] [synopsis: Place copies of model on polygons of cage]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-RotamerLibsRichardson (installed) [version: 2.0] [api package: chimerax.richardson_rotamer_lib] [category: Structure Editing] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-PDB (installed) [version: 2.7.6] [api package: chimerax.pdb] [category: Molecular structure] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-BILD (installed) [version: 1.0] [api package: chimerax.bild] [category: Generic 3D objects] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Zone (installed) [version: 1.0.1] [api package: chimerax.zone] [category: Volume Data] [command: zone [categories: Volume data] [synopsis: Show atoms and map in a small region]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-WebCam (installed) [version: 1.0.2] [api package: chimerax.webcam] [category: General] [command: webcam [categories: General] [synopsis: Show webcam video]] [command: device webcam [categories: General] [synopsis: Show webcam video]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Test (installed) [version: 1.0] [api package: chimerax.test] [category: General] [command: debug test [categories: General] [synopsis: Run through test sequence of commands to check for errors]] [command: debug exectest [categories: General] [synopsis: Test running executable from bundle]] [command: debug expectfail [categories: General] [synopsis: Expect command to fail]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-SeqView (installed) [version: 2.14] [api package: chimerax.seq_view] [category: Sequence] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-SDF (installed) [version: 2.0.2] [api package: chimerax.sdf] [category: Atomic Data] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-RemoteControl (installed) [version: 1.0] [api package: chimerax.remote_control] [category: General] [command: remotecontrol xmlrpc [categories: General] [synopsis: synopsis]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-MutationScores (installed) [version: 1.0] [api package: chimerax.mutation_scores] [category: Molecular structure] [command: mutationscores label [categories: Molecular structure] [synopsis: Label residues with mutation scores]] [command: mutationscores define [categories: Molecular structure] [synopsis: Compute new scores from existing mutation scores]] [command: mutationscores undefine [categories: Molecular structure] [synopsis: Compute new scores from existing mutation scores]] [command: mutationscores scatterplot [categories: Molecular structure] [synopsis: Show a scatter plot for two mutations scores]] [command: mutationscores statistics [categories: Molecular structure] [synopsis: Report mean and standard deviation of mutation scores]] [command: mutationscores histogram [categories: Molecular structure] [synopsis: Show histogram of mutation scores]] [command: mutationscores umap [categories: Molecular structure] [synopsis: Show umap plot of residue mutation scores]] [command: mutationscores list [categories: Molecular structure] [synopsis: List names of sets of mutations scores]] [command: mutationscores structure [categories: Molecular structure] [synopsis: Associate a structure with a set of mutations scores]] [command: mutationscores close [categories: Molecular structure] [synopsis: Close a set of mutations scores]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-IO (installed) [version: 1.0.3] [api package: chimerax.io] [category: Input/Output] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-DockPrep (installed) [version: 1.1.3] [api package: chimerax.dock_prep] [category: Structure Editing] [tool: Dock Prep [categories: Structure Editing] [synopsis: prepare structures for docking]] [command: dockprep [categories: Structure Editing] [synopsis: prepare structures for docking]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Movie (installed) [version: 1.0] [api package: chimerax.movie] [category: General] [command: movie [categories: General] [synopsis: record movies]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Clashes (installed) [version: 2.3] [api package: chimerax.clashes] [category: Structure Analysis] [tool: Clashes [categories: Structure Analysis] [synopsis: Find atom-atom clashes]] [tool: Contacts [categories: Structure Analysis] [synopsis: Find atom-atom contacts]] [command: clashes [categories: Structure Analysis] [synopsis: Find atoms with steric clashes]] [command: contacts [categories: Structure Analysis] [synopsis: Finds atoms in contact with one another]] [command: ~clashes [categories: Structure Analysis] [synopsis: Clear clash pseudobond]] [command: ~contacts [categories: Structure Analysis] [synopsis: Clear contact pseudobond]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-mmCIF (installed) [version: 2.14.2] [api package: chimerax.mmcif] [category: Molecular structure] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-uniprot (installed) [version: 2.3.1] [api package: chimerax.uniprot] [category: Sequence] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Morph (installed) [version: 1.0.2] [api package: chimerax.morph] [category: Morph Structures] [command: morph [categories: Molecular structure] [synopsis: morph atomic structures]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Umap (installed) [version: 1.0] [api package: chimerax.umap] [category: Utilities] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-coulombic (installed) [version: 1.4.4] [api package: chimerax.coulombic] [category: Surface/Binding Analysis] [command: coulombic [categories: Surface/Binding Analysis] [synopsis: Color surface based on electrostatics]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-BugReporter (installed) [version: 1.0.1] [api package: chimerax.bug_reporter] [category: General] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-PresetMgr (installed) [version: 1.1.2] [api package: chimerax.preset_mgr] [category: Depiction] [command: preset [categories: Depiction] [synopsis: apply "preset" depiction to models]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Crosslinks (installed) [version: 1.0] [api package: chimerax.crosslinks] [category: General] [command: crosslinks [categories: General] [synopsis: Plot or minimize crosslink lengths]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-OpenCommand (installed) [version: 1.14] [api package: chimerax.open_command] [category: Commands] [command: open [categories: General] [synopsis: Open/fetch data files]] [command: usage open [categories: General] [synopsis: Show syntax of 'open' command]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-ShowSequences (installed) [version: 1.0.3] [api package: chimerax.show_sequences] [category: Sequence] [tool: Show Sequence Viewer [categories: Sequence] [synopsis: show chain sequences]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Markers (installed) [version: 1.0.1] [api package: chimerax.markers] [category: Volume Data] [tool: Marker Placement [categories: Volume Data] [synopsis: Place markers on density maps]] [command: marker [categories: General] [synopsis: Place markers]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-SaveCommand (installed) [version: 1.5.1] [api package: chimerax.save_command] [category: Commands] [command: save [categories: General] [synopsis: Save data files]] [command: usage save [categories: General] [synopsis: Show 'save' command syntax]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-ResidueFit (installed) [version: 1.0.1] [api package: chimerax.residue_fit] [category: General] [command: resfit [categories: General] [synopsis: Display slider to show fit of each residue in density map]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-SpaceNavigator (installed) [version: 1.0] [api package: chimerax.spacenavigator] [category: General] [command: device snav [categories: General] [synopsis: Control SpaceNavigator device]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-AddH (installed) [version: 2.2.6] [api package: chimerax.addh] [category: Structure Editing] [tool: Add Hydrogens [categories: Structure Editing] [synopsis: Add hydrogens to structure]] [command: addh [categories: Structure Editing] [synopsis: Add hydrogens]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-ColorActions (installed) [version: 1.0.5] [api package: chimerax.color_actions] [category: Depiction] [tool: Color Actions [categories: Depiction] [synopsis: color items]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-AmberInfo (installed) [version: 1.0] [api package: chimerax.amber_info] [category: Structure Editing] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-ButtonPanel (installed) [version: 1.0.1] [api package: chimerax.buttonpanel] [category: General] [command: buttonpanel [categories: General] [synopsis: Create custom user interface panels]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-PDBMatrices (installed) [version: 1.0] [api package: chimerax.pdb_matrices] [category: Molecular structure] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-RNALayout (installed) [version: 1.0] [api package: chimerax.rna_layout] [category: Structure Editing] [command: rna path [categories: Structure Editing] [synopsis: make RNA marker model]] [command: rna model [categories: Structure Editing] [synopsis: make RNA atomic model]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-IHM (installed) [version: 1.1] [api package: chimerax.ihm] [category: Higher-Order Structure] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Shortcuts (installed) [version: 1.2.0] [api package: chimerax.shortcuts] [category: Toolbar] [command: ks [categories: Toolbar] [synopsis: keyboard shortcuts]] [command: snapshot [categories: Toolbar] [synopsis: Save graphics image]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Contacts (installed) [version: 1.0.1] [api package: chimerax.interfaces] [category: Molecular structure] [command: interfaces [categories: Molecular structure] [synopsis: Display chain contact maps]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Vive (installed) [version: 1.1] [api package: chimerax.vive] [category: General] [command: vr [categories: General] [synopsis: Render to virtual reality headsets using SteamVR]] [command: xr [categories: General] [synopsis: Render to virtual reality headsets using OpenXR]] [command: device vr [categories: General] [synopsis: Render to virtual reality headsets]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-PDBLibrary (installed) [version: 1.0.4] [api package: chimerax.pdb_lib] [category: Molecular structure] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-SmoothLines (installed) [version: 1.0] [api package: chimerax.smooth_lines] [category: General] [command: smoothlines [categories: General] [synopsis: Smooth networks of lines]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-AtomSearch (installed) [version: 2.0.1] [api package: chimerax.atom_search] [category: Structure Analysis] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-EMDB-SFF (installed) [version: 1.0] [api package: chimerax.emdb_sff] [category: Volume Data] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-NMRSTAR (installed) [version: 1.0.2] [api package: chimerax.nmrstar] [category: Generic 3D objects] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Shape (installed) [version: 1.0.1] [api package: chimerax.shape] [category: Generic 3D objects] [command: shape boxPath [categories: Surfaces] [synopsis: create a box beam model]] [command: shape cone [categories: Surfaces] [synopsis: create a cone model]] [command: shape cylinder [categories: Surfaces] [synopsis: create a cylinder model]] [command: shape ellipsoid [categories: Surfaces] [synopsis: create an ellipsoid model]] [command: shape icosahedron [categories: Surfaces] [synopsis: create a icosahedron model]] [command: shape rectangle [categories: Surfaces] [synopsis: create a rectangle model]] [command: shape ribbon [categories: Surfaces] [synopsis: create a ribbon model]] [command: shape sphere [categories: Surfaces] [synopsis: create a sphere model]] [command: shape triangle [categories: Surfaces] [synopsis: create a triangle model]] [command: shape tube [categories: Surfaces] [synopsis: create a tube model]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-ConnectStructure (installed) [version: 2.0.1] [api package: chimerax.connect_structure] [category: Structure Analysis] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-ToQuest (installed) [version: 1.0] [api package: chimerax.to_quest] [category: General] [tool: Send to Quest [categories: General] [synopsis: Send scenes to Quest headset Lookie app]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Arrays (installed) [version: 1.1] [api package: chimerax.arrays] [category: Utility] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-NRRD (installed) [version: 1.2] [api package: chimerax.nrrd] [category: Volume Data] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Tug (installed) [version: 1.0.1] [api package: chimerax.tug] [category: Molecular structure] [command: tug [categories: tug an atom using molecular dynamics] [synopsis: No synopsis given]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Label (installed) [version: 1.1.14] [api package: chimerax.label] [category: General] [tool: Scale Bar [categories: Depiction] [synopsis: Show a scale bar]] [command: 2dlabels [categories: General] [synopsis: add text labels to graphics]] [command: scalebar [categories: General] [synopsis: show a scalebar]] [command: label [categories: General] [synopsis: add 3d labels to graphics]] [command: ~label [categories: General] [synopsis: remove 3d labels from graphics]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-VTK (installed) [version: 1.0] [api package: chimerax.vtk] [category: Generic 3D objects] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-MLP (installed) [version: 1.1.1] [api package: chimerax.mlp] [category: Molecular structure] [command: mlp [categories: Molecular structure] [synopsis: Molecular lipophilicity calculation]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Crystal (installed) [version: 1.0] [api package: chimerax.crystal] [category: Generic 3D objects] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-MapSeries (installed) [version: 2.1.1] [api package: chimerax.map_series] [category: Volume Data] [command: vseries [categories: Volume data] [synopsis: volume series]] [command: measure motion [categories: Volume data] [synopsis: volume series cactus prickles]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-TapeMeasure (installed) [version: 1.0] [api package: chimerax.tape_measure] [category: General] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Smiles (installed) [version: 2.1.2] [api package: chimerax.smiles] [category: Molecular structure] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Dicom (installed) [version: 1.2.6] [api package: chimerax.dicom] [category: Medical Imaging] [tool: DICOM Browser [categories: Medical Imaging] [synopsis: View the metadata of a patient's DICOM files]] [tool: Download DICOM [categories: Medical Imaging] [synopsis: View the contents of public DICOM datasets from within ChimeraX]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-ImageFormats (installed) [version: 1.2] [api package: chimerax.image_formats] [category: I/O] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-CrystalContacts (installed) [version: 1.0.1] [api package: chimerax.crystal_contacts] [category: Higher-Order Structure] [tool: Crystal Contacts [categories: Higher-Order Structure] [synopsis: Show contacting subunits in a crystal]] [command: crystalcontacts [categories: Higher-Order Structure] [synopsis: Make contacting copies of a crystal asymmetric unit]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-SideView (installed) [version: 1.0.1] [api package: chimerax.sideview] [category: General] [tool: Side View [categories: General] [synopsis: Show side view interface]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-STL (installed) [version: 1.0.1] [api package: chimerax.stl] [category: Generic 3D objects] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-MDcrds (installed) [version: 2.7.2] [api package: chimerax.md_crds] [category: Molecular Dynamics] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Hbonds (installed) [version: 2.5] [api package: chimerax.hbonds] [category: Structure Analysis] [tool: H-Bonds [categories: Structure Analysis] [synopsis: Find hydrogen bonds]] [command: hbonds [categories: Structure Analysis] [synopsis: Find hydrogen bonds]] [command: ~hbonds [categories: Structure Analysis] [synopsis: Clear hydrogen bonds]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-WavefrontOBJ (installed) [version: 1.0] [api package: chimerax.wavefront_obj] [category: Generic 3D objects] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-RotamerLibsDynameomics (installed) [version: 2.0] [api package: chimerax.dynameomics_rotamer_lib] [category: Structure Editing] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-BondRot (installed) [version: 2.0.4] [api package: chimerax.bond_rot] [category: Structure Editing] [command: torsion [categories: Report or set torsion angle] [synopsis: Report torsion angle of 4 atoms, or set it (middle two atoms must be bonded for setting)]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Surface (installed) [version: 1.0.1] [api package: chimerax.surface] [category: Generic 3D objects] [tool: Hide Dust [categories: Volume Data] [synopsis: hide small surface blobs]] [tool: Surface Zone [categories: Volume Data] [synopsis: show surface near atoms]] [tool: Color Zone [categories: Volume Data] [synopsis: color surface to match nearby atoms]] [tool: Measure Volume and Area [categories: Volume Data] [synopsis: measure surface area and enclosed volume]] [tool: Surface Color [categories: Volume Data, Depiction] [synopsis: Color surface by geometry or map value]] [command: color electrostatic [categories: Surfaces] [synopsis: color surface by electrostatic potential map]] [command: color sample [categories: Surfaces] [synopsis: color surface by map value]] [command: color gradient [categories: Surfaces] [synopsis: color surface by map gradient norm]] [command: color radial [categories: Surfaces] [synopsis: color surface by distance from a point]] [command: color cylindrical [categories: Surfaces] [synopsis: color surface by distance from an axis]] [command: color height [categories: Surfaces] [synopsis: color surface by distance from a plane]] [command: color image [categories: Surfaces] [synopsis: color surface using an image file]] [command: surface [categories: Surfaces] [synopsis: create/modify surfaces]] [command: ~surface [categories: Surfaces] [synopsis: delete surface]] [command: surface showPatches [categories: Surfaces] [synopsis: show atom surface patches for existing surfaces]] [command: surface hidePatches [categories: Surfaces] [synopsis: hide patches of existing surfaces for specified atoms]] [command: surface close [categories: Surfaces] [synopsis: close surfaces for specified atoms]] [command: surface style [categories: Surfaces] [synopsis: set surface mesh, solid, or dot display style]] [command: surface squaremesh [categories: Surfaces] [synopsis: mask mesh lines that are not parallel x, y or z]] [command: surface showall [categories: Surfaces] [synopsis: turn of maskig of triangles and edges]] [command: surface cap [categories: Surfaces] [synopsis: control surface caps when clipping]] [command: surface dust [categories: Surfaces] [synopsis: hide small pieces of surfaces]] [command: surface undust [categories: Surfaces] [synopsis: show small pieces of surfaces]] [command: surface hidefarblobs [categories: Surfaces] [synopsis: hide connected pieces of a surface that are far from another surface]] [command: surface invertShown [categories: Surfaces] [synopsis: Show hidden part of surface and hide shown part]] [command: surface transform [categories: Surfaces] [synopsis: Scale, rotate or move surfaces]] [command: surface zone [categories: Surfaces] [synopsis: show surface near atoms]] [command: surface unzone [categories: Surfaces] [synopsis: show all of surface]] [command: surface check [categories: Surfaces] [synopsis: check surface topology]] [command: surface splitbycolor [categories: Surfaces] [synopsis: Split surface by color]] [command: sop [categories: Surfaces] [synopsis: alias for surface commands]] [command: volume splitbyzone [categories: Volume Data] [synopsis: split volume by color zone]] [command: measure sasa [categories: Surfaces] [synopsis: measure solvent-accessible surface area]] [command: measure volume [categories: Surfaces] [synopsis: measure enclosed surface volume]] [command: measure area [categories: Surfaces] [synopsis: measure surface area]] [command: measure contactArea [categories: Surfaces] [synopsis: measure and contact area between two surfaces]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-MapFit (installed) [version: 2.0] [api package: chimerax.map_fit] [category: Volume Data] [tool: Fit in Map [categories: Volume Data] [synopsis: Fit molecules in maps]] [command: fitmap [categories: Volume data] [synopsis: fit molecules in maps]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Graphics (installed) [version: 1.4.1] [api package: chimerax.graphics] [category: Graphics] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-FileHistory (installed) [version: 1.0.1] [api package: chimerax.file_history] [category: General] [tool: File History [categories: General] [synopsis: Show recently opened files]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-ViewDockX (installed) [version: 1.4.4] [api package: chimerax.viewdockx] [category: General] [tool: ViewDockX [categories: Binding Analysis] [synopsis: display docking results]] [command: viewdockx [categories: Binding Analysis] [synopsis: specify models as docking results]] [command: viewdockx down [categories: Binding Analysis] [synopsis: Simulate down-arrow key in ViewDockX]] [command: viewdockx up [categories: Binding Analysis] [synopsis: Simulate up-arrow key in ViewDockX]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-BlastProtein (installed) [version: 3.0.0] [api package: chimerax.blastprotein] [category: Sequence] [tool: Blast Protein [categories: Sequence] [synopsis: Search PDB/NR/AlphaFold using BLAST]] [command: blastprotein [categories: Sequence] [synopsis: Search PDB/NR/AlphaFold using BLAST]] [command: blastpdb [categories: Sequence] [synopsis: Search PDB/NR/AlphaFold using BLAST]] [command: blastprotein pull [categories: Sequence] [synopsis: Get results for a finished BlastProtein job]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Positions (installed) [version: 1.0] [api package: chimerax.positions] [category: Generic 3D objects] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-CellPack (installed) [version: 1.0] [api package: chimerax.cellpack] [category: Molecular structure] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Toolbar (installed) [version: 1.2.3] [api package: chimerax.toolbar] [category: General] [tool: Toolbar [categories: General] [synopsis: a Windows ribbon-style toolbar]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Maestro (installed) [version: 1.9.1] [api package: chimerax.maestro] [category: I/O] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-AtomicLibrary (installed) [version: 14.1.11] [api package: chimerax.atomic_lib] [category: Structure Analysis, Structure Editing] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-PubChem (installed) [version: 2.2] [api package: chimerax.pubchem] [category: Molecular structure] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-UI (installed) [version: 1.41] [api package: chimerax.ui] [category: User Interface] [command: ui [categories: User interface] [synopsis: control user interface behavior]] [command: tool [categories: User interface] [synopsis: Manipulate tools]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-PickBlobs (installed) [version: 1.0.1] [api package: chimerax.pick_blobs] [category: Volume data] [tool: Measure and Color Blobs [categories: Volume Data] [synopsis: Measure and color connected parts of surfaces]] [command: measure blob [categories: Measure and Color Blobs] [synopsis: Measure and color connected parts of surfaces]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-WebServices (installed) [version: 1.1.4] [api package: chimerax.webservices] [category: General] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-LinuxSupport (installed) [version: 1.0.1] [api package: chimerax.linux] [category: General] [command: linux xdg-install [categories: General] [synopsis: Integrate ChimeraX with Linux desktop]] [command: linux xdg-uninstall [categories: General] [synopsis: Remove integration with Linux desktop]] [command: linux flatpak-files [categories: General] [synopsis: Generate flatpak metainfo and desktop files]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-PDBBio (installed) [version: 1.0.1] [api package: chimerax.pdb_bio] [category: Molecular structure] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-SchemeMgr (installed) [version: 1.0] [api package: chimerax.scheme_mgr] [category: Utilities] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-CoreFormats (installed) [version: 1.2] [api package: chimerax.core_formats] [category: Atomic Data] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Core (installed) [version: 1.9] [api package: chimerax.core] [category: Core] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-MouseModes (installed) [version: 1.2] [api package: chimerax.mouse_modes] [category: Toolbar] [command: ui mousemode [categories: User interface] [synopsis: set/list mouse modes]] [command: mousemode [categories: User interface] [synopsis: set/list mouse modes]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-CommandLine (installed) [version: 1.2.5] [api package: chimerax.cmd_line] [category: General] [tool: Command Line Interface [categories: General] [synopsis: Command Line Interface]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-ChemGroup (installed) [version: 2.0.1] [api package: chimerax.chem_group] [category: Structure Analysis] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-MapEraser (installed) [version: 1.0.1] [api package: chimerax.map_eraser] [category: Volume data] [tool: Map Eraser [categories: Volume Data] [synopsis: Erase part of a density map within a sphere]] [command: volume erase [categories: Erase image data] [synopsis: Erase part of a density map within a sphere]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-SwapRes (installed) [version: 2.5] [api package: chimerax.swap_res] [category: Structure Editing] [tool: Rotamers [categories: Structure Editing] [synopsis: swap amino acid residue side chain]] [command: swapaa [categories: Structure Editing] [synopsis: swap amino acid residue side chain]] [command: swapna [categories: Structure Editing] [synopsis: swap nucleic acid residue side chain]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-MatchMaker (installed) [version: 2.1.6] [api package: chimerax.match_maker] [category: Sequence] [tool: Matchmaker [categories: Structure Analysis] [synopsis: superimpose structures/chains]] [command: matchmaker [categories: Structure Comparison] [synopsis: Superimpose structures]] [command: mmaker [categories: Structure Analysis] [synopsis: alias of matchmaker]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Shell (installed) [version: 1.0.1] [api package: chimerax.shell] [category: General] [tool: Shell [categories: General] [synopsis: Python shell]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Bumps (installed) [version: 1.0] [api package: chimerax.bumps] [category: Volume Data] [command: bumps [categories: Volume Data] [synopsis: find protrusions in density maps]] [command: cbumps [categories: Volume Data] [synopsis: find convex surface patches]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-RenderByAttr (installed) [version: 1.6.2] [api package: chimerax.render_by_attr] [category: Depiction, Structure Analysis] [tool: Render/Select by Attribute [categories: Structure Analysis, Depiction] [synopsis: depict attribute values on structures]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-RenumberResidues (installed) [version: 1.1] [api package: chimerax.renumber_residues] [category: Structure Editing] [tool: Renumber Residues [categories: Structure Editing] [synopsis: renumber residues]] [command: renumber [categories: Structure Editing] [synopsis: renumber residues]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-AlphaFold (installed) [version: 1.0.1] [api package: chimerax.alphafold] [category: Structure Prediction] [tool: AlphaFold [categories: Structure Prediction] [synopsis: Fetch or calculate AlphaFold structures]] [tool: AlphaFold Error Plot [categories: Structure Prediction] [synopsis: Plot AlphaFold predicted aligned error]] [command: alphafold match [categories: Structure Prediction] [synopsis: Fetch AlphaFold database models matching a structure]] [command: alphafold fetch [categories: Structure Prediction] [synopsis: Fetch AlphaFold database models for a UniProt identifier]] [command: alphafold search [categories: Structure Prediction] [synopsis: Search AlphaFold database using BLAST]] [command: alphafold predict [categories: Structure Prediction] [synopsis: Predict a structure using AlphaFold]] [command: alphafold pae [categories: Structure Prediction] [synopsis: Show AlphaFold predicted aligned error as heatmap]] [command: alphafold contacts [categories: Structure Prediction] [synopsis: Show AlphaFold contact pseudobond colored by predicted aligned error]] [command: alphafold dimers [categories: Structure Prediction] [synopsis: Setup AlphaFold dimer predictions]] [command: alphafold monomers [categories: Structure Prediction] [synopsis: Estimate time for AlphaFold predictions]] [command: alphafold interfaces [categories: Structure Prediction] [synopsis: Evaluate AlphaFold PAE scores at dimer interfaces]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-RotamerLibsDunbrack (installed) [version: 2.0] [api package: chimerax.dunbrack_rotamer_lib] [category: Structure Editing] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-ColorKey (installed) [version: 1.5.6] [api package: chimerax.color_key] [category: Depiction] [tool: Color Key [categories: Depiction] [synopsis: add color key to graphics]] [command: key [categories: General] [synopsis: add color key to graphics]] [command: ~key [categories: General] [synopsis: remove color key]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-ReadPbonds (installed) [version: 1.0.1] [api package: chimerax.read_pbonds] [category: Generic 3D objects] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-ModelPanel (installed) [version: 1.5] [api package: chimerax.model_panel] [category: General] [tool: Model Panel [categories: General] [synopsis: model panel]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-HKCage (installed) [version: 1.3] [api package: chimerax.hkcage] [category: Higher-Order Structure] [command: hkcage [categories: Higher-Order Structure] [synopsis: Create icosahedral cage]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Map (installed) [version: 1.3] [api package: chimerax.map] [category: Volume Data] [tool: Volume Viewer [categories: Volume Data] [synopsis: Show density maps info]] [tool: Map Coordinates [categories: Volume Data] [synopsis: Adjust density map coordinates]] [tool: Map Statistics [categories: Volume Data] [synopsis: Report map minimum, maximum, mean, standard deviation, and root mean square]] [command: volume [categories: Volume data] [synopsis: control volume data display]] [command: molmap [categories: Volume data] [synopsis: create density map for molecule]] [command: measure mapstats [categories: Volume data] [synopsis: report map statistics]] [command: measure mapvalues [categories: Volume data] [synopsis: Intepolate map at atom positions]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Meeting (installed) [version: 1.0.1] [api package: chimerax.meeting] [category: General] [tool: Meeting [categories: General] [synopsis: Multi-person sessions]] [command: meeting start [categories: General] [synopsis: Create a ChimeraX meeting]] [command: meeting join [categories: General] [synopsis: Join a ChimeraX meeting]] [command: meeting [categories: General] [synopsis: Same as meeting join]] [command: meeting close [categories: General] [synopsis: Close a ChimeraX meeting]] [command: meeting info [categories: General] [synopsis: Report ChimeraX meeting info]] [command: meeting settings [categories: General] [synopsis: Report or set meeting default settings]] [command: meeting server [categories: General] [synopsis: Report or define meeting server names]] [command: meeting unname [categories: General] [synopsis: Deregister a meeting name]] [command: meeting send [categories: General] [synopsis: Copy my scene to all other meeting participants]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-AltlocExplorer (installed) [version: 1.1.2] [api package: chimerax.altloc_explorer] [category: Structure Analysis] [tool: Altloc Explorer [categories: Structure Analysis] [synopsis: interact with alternate atom locations]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Struts (installed) [version: 1.0.1] [api package: chimerax.struts] [category: Molecular structure] [command: struts [categories: Molecular structure] [synopsis: provide struts for 3D printing]] [command: ~struts [categories: Molecular structure] [synopsis: remove 3D printing struts]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-DistMonitor (installed) [version: 1.4.2] [api package: chimerax.dist_monitor] [category: Structure Analysis] [command: distance [categories: Structure Analysis] [synopsis: determine distance]] [command: ~distance [categories: Structure Analysis] [synopsis: remove distance monitors]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Mask (installed) [version: 1.0.2] [api package: chimerax.mask] [category: Volume Data] [command: volume mask [categories: Volume data] [synopsis: Mask a map to a surface]] [command: volume onesmask [categories: Volume data] [synopsis: Create a onesmask inside a surface]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Registration (installed) [version: 1.1.2] [api package: chimerax.registration] [category: Utilities] [tool: Registration [categories: Utilities] [synopsis: Register ChimeraX with RBVI]] [command: registration status [categories: Utilities] [synopsis: Report registration status]] [command: registration file [categories: Utilities] [synopsis: Report registration file location or apply registration file]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-StdCommands (installed) [version: 1.18.1] [api package: chimerax.std_commands] [category: Structure Analysis] [command: alias [categories: General Controls] [synopsis: create shorthand version of command]] [command: alias list [categories: General Controls] [synopsis: list command aliases]] [command: alias delete [categories: General Controls] [synopsis: remove command alias]] [command: ~alias [categories: General Controls] [synopsis: remove command alias]] [command: align [categories: Structure Comparison] [synopsis: superimpose specific parts of structures]] [command: altlocs [categories: Structure Editing] [synopsis: change/remove alternate atom locations]] [command: angle [categories: Structure Analysis] [synopsis: Report or set angle between atoms/objects]] [command: camera [categories: Viewing Controls] [synopsis: change "camera" parametrs of main viewing window]] [command: cartoon [categories: Depiction] [synopsis: show stylized representation of structure]] [command: ~cartoon [categories: Depiction] [synopsis: stop show stylized representation of structure]] [command: cd [categories: General Controls] [synopsis: change ChimeraX's current working directory]] [command: clip [categories: Viewing Controls] [synopsis: control clipping of models]] [command: ~clip [categories: Viewing Controls] [synopsis: stop clipping of models]] [command: close [categories: General Controls] [synopsis: close models]] [command: cofr [categories: General Controls] [synopsis: set center of rotation]] [command: ~cofr [categories: General Controls] [synopsis: revert to default center of rotation]] [command: color [categories: Depiction] [synopsis: change model colors]] [command: colour [categories: Depiction] [synopsis: change model colors]] [command: color delete [categories: General Controls] [synopsis: delete custom color names]] [command: color list [categories: General Controls] [synopsis: list custom color names]] [command: color name [categories: General Controls] [synopsis: define custom color names]] [command: color show [categories: General Controls] [synopsis: show definition of custom color names]] [command: colordef [categories: General Controls] [synopsis: define custom color names]] [command: ~colordef [categories: General Controls] [synopsis: remove custom color names]] [command: colourdef [categories: General Controls] [synopsis: define custom color names]] [command: ~colourdef [categories: General Controls] [synopsis: remove custom color names]] [command: coordset [categories: General Controls] [synopsis: show specific coordinate set (a.k.a. frame or conformer)]] [command: crossfade [categories: Movie Making] [synopsis: fade from one view to another]] [command: defattr [categories: General Controls] [synopsis: set many Python attribute values for structure elements from a file]] [command: delete [categories: Structure Editing] [synopsis: delete parts of a structure]] [command: dssp [categories: Structure Editing] [synopsis: compute/assign secondary structure]] [command: exit [categories: General Controls] [synopsis: quit ChimeraX]] [command: quit [categories: General Controls] [synopsis: quit ChimeraX]] [command: fly [categories: General Controls] [synopsis: interpolate motions for animations]] [command: getcrd [categories: General] [synopsis: report atomic coordinates]] [command: graphics [categories: General Controls] [synopsis: control 3D graphics parameters]] [command: hide [categories: Viewing Controls] [synopsis: stop displaying (parts of) a model]] [command: ~show [categories: Viewing Controls] [synopsis: stop displaying (parts of) a model]] [command: ~display [categories: Viewing Controls] [synopsis: stop displaying (parts of) a model]] [command: lighting [categories: Viewing Controls] [synopsis: change lighting]] [command: lighting model [categories: Viewing Controls] [synopsis: change per-model lighting]] [command: material [categories: Depiction] [synopsis: change visual surface properties of 3D objects]] [command: measure buriedarea [categories: Surface/Binding Analysis] [synopsis: measure surface area buried by contacting structures]] [command: measure center [categories: Volume] [synopsis: measure center of mass of maps or atoms]] [command: measure convexity [categories: Surface/Binding Analysis] [synopsis: color surface based on local convexity]] [command: measure correlation [categories: Volume] [synopsis: measure correlation coefficient between two maps]] [command: measure inertia [categories: General Controls] [synopsis: measure moments of inertia]] [command: measure length [categories: Volume] [synopsis: measure path length of connected markers]] [command: measure rotation [categories: Volume] [synopsis: measure rotation of one model relative to another]] [command: measure symmetry [categories: Volume] [synopsis: compute map symmetry]] [command: measure weight [categories: Structure Analysis] [synopsis: measure molecular weight of specified atoms]] [command: move [categories: General Controls] [synopsis: move (parts of) a model relative to others]] [command: move cofr [categories: General Controls] [synopsis: move models to center of rotation]] [command: palette [categories: General Controls] [synopsis: list available color palettes]] [command: perframe [categories: General Controls] [synopsis: execute commands every frame]] [command: ~perframe [categories: General Controls] [synopsis: stop execution of commands every frame]] [command: pwd [categories: Utilities] [synopsis: report current working directory]] [command: rainbow [categories: Depiction] [synopsis: "rainbow" color (parts of) structures]] [command: rename [categories: General Controls] [synopsis: change name or ID of model]] [command: ribbon [categories: Depiction] [synopsis: show stylized representation of structure]] [command: ~ribbon [categories: Depiction] [synopsis: stop show stylized representation of structure]] [command: rmsd [categories: Structure Comparison] [synopsis: measure RMSD between two sets of atoms]] [command: rock [categories: General Controls] [synopsis: rock models back and forth]] [command: roll [categories: General Controls] [synopsis: continuously turn model(s) about an axis]] [command: runscript [categories: General Controls] [synopsis: run a Python script with arguments]] [command: select [categories: General Controls] [synopsis: select models or parts thereof]] [command: ~select [categories: General Controls] [synopsis: unselect models or parts thereof]] [command: set [categories: General Controls] [synopsis: set various global parameters]] [command: ~set [categories: General Controls] [synopsis: revert various global parameters to their default value]] [command: setattr [categories: General Controls] [synopsis: set Python attribute values for structure elements]] [command: show [categories: Viewing Controls] [synopsis: display (parts of) a model]] [command: display [categories: Viewing Controls] [synopsis: display (parts of) a model]] [command: size [categories: Depiction] [synopsis: change display size of structural elements]] [command: split [categories: General Controls] [synopsis: split a model into multiple models]] [command: stop [categories: General Controls] [synopsis: stop an ongoing motion]] [command: style [categories: Depiction] [synopsis: change style of depiction for strcutural elements]] [command: sym [categories: Higher-Order Structure] [synopsis: generate symmetry mates]] [command: tile [categories: General Controls] [synopsis: tile models onto grid]] [command: ~tile [categories: General Controls] [synopsis: untile models]] [command: time [categories: Utilities] [synopsis: time execution and redisplay of commands]] [command: transparency [categories: Depiction] [synopsis: change transparency of (parts of) models]] [command: turn [categories: General Controls] [synopsis: rotate a model about an axis]] [command: undo [categories: General Controls] [synopsis: undo a command]] [command: redo [categories: General Controls] [synopsis: redo an undone command]] [command: usage [categories: Utilities] [synopsis: show the required syntax for a command]] [command: version [categories: Utilities] [synopsis: report ChimeraX version number]] [command: view [categories: Viewing Controls] [synopsis: change/save/restore 3D view]] [command: wait [categories: Movie Making] [synopsis: wait a given amount of frames before executing the next command]] [command: windowsize [categories: General Controls] [synopsis: set the size of the 3D window]] [command: wobble [categories: General Controls] [synopsis: move models in figure 8 motion]] [command: worm [categories: General Controls] [synopsis: turn on/off worm depiction]] [command: ~worm [categories: General Controls] [synopsis: turn off worm depiction]] [command: select zone [categories: General Controls] [synopsis: select (parts of) models within a 3D zone]] [command: zoom [categories: Viewing Controls] [synopsis: zoom in/out]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-AlignmentAlgorithms (installed) [version: 2.0.2] [api package: chimerax.alignment_algs] [category: Sequence alignment] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-IMOD (installed) [version: 1.0] [api package: chimerax.imod] [category: Volume Data] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-ToolshedUtils (installed) [version: 1.2.4] [api package: chimerax.toolshed_utils] [category: Utilities] [tool: Updates [categories: Utilities] [synopsis: install/update ChimeraX bundles from the Toolshed (web repository)]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-Segger (installed) [version: 1.0] [api package: chimerax.segger] [category: Volume data] [tool: Segment Map [categories: Volume Data] [synopsis: Segment density maps using Segger algorithms]] [tool: Fit to Segments [categories: Volume Data] [synopsis: Fit atomic models in segmented maps]] [command: segger [categories: Volume data] [synopsis: Operate on Segger segmentations]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-MapData (installed) [version: 2.0] [api package: chimerax.map_data] [category: Volume Data] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-KVFinder (installed) [version: 1.2.1] [api package: chimerax.kvfinder] [category: Binding Analysis, Structure Analysis] [tool: Find Cavities [categories: Binding Analysis, Structure Analysis] [synopsis: Find potential binding pockets]] [command: kvfinder [categories: Binding Analysis] [synopsis: Find pockets]] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-RotamerLibMgr (installed) [version: 4.0] [api package: chimerax.rotamers] [category: Structure Editing] Toolshed: InstalledBundleCache.load: package Toolshed: InstalledBundleCache.load: bundle ChimeraX-OrthoPick (installed) [version: 1.0.1] [api package: chimerax.orthopick] [category: Volume data] [tool: Orthopick [categories: Volume Data] [synopsis: Pick particles in tomograms]] Toolshed: InstalledBundleCache.load: write_cache Toolshed: InstalledBundleCache._write_cache /home/jobilinux/.cache/ChimeraX/1.9/toolshed/bundle_info.cache Toolshed: register bundle ChimeraX-Core 1.9 Toolshed: register bundle ChimeraX-ToolshedUtils 1.2.4 Toolshed: register bundle ChimeraX-Arrays 1.1 Toolshed: register bundle ChimeraX-AtomicLibrary 14.1.11 Toolshed: register bundle ChimeraX-Umap 1.0 Toolshed: register bundle ChimeraX-PresetMgr 1.1.2 Toolshed: delay_registration preset Toolshed: register bundle ChimeraX-RemoteControl 1.0 Toolshed: delay_registration remotecontrol xmlrpc Toolshed: register bundle ChimeraX-IO 1.0.3 Toolshed: register bundle ChimeraX-ListInfo 1.2.2 Toolshed: delay_registration info Toolshed: register bundle ChimeraX-SimilarStructures 1.0.1 Toolshed: delay_registration foldseek Toolshed: delay_registration similarstructures open Toolshed: delay_registration similarstructures close Toolshed: delay_registration similarstructures list Toolshed: delay_registration similarstructures sequences Toolshed: delay_registration similarstructures traces Toolshed: delay_registration similarstructures cluster Toolshed: delay_registration similarstructures ligands Toolshed: delay_registration similarstructures scrollto Toolshed: delay_registration similarstructures pairing Toolshed: delay_registration similarstructures seqalign Toolshed: delay_registration similarstructures fetchcoords Toolshed: delay_registration sequence search Toolshed: delay_registration similarstructures blast Toolshed: delay_registration similarstructures fromblast Toolshed: register bundle ChimeraX-Movie 1.0 Toolshed: delay_registration movie Toolshed: register bundle ChimeraX-Geometry 1.3 Toolshed: register bundle ChimeraX-RestServer 1.3.1 Toolshed: delay_registration remotecontrol rest Toolshed: register bundle ChimeraX-Test 1.0 Toolshed: delay_registration debug test Toolshed: delay_registration debug exectest Toolshed: delay_registration debug expectfail Toolshed: register bundle ChimeraX-WebServices 1.1.4 Toolshed: register bundle ChimeraX-RotamerLibMgr 4.0 Toolshed: register bundle ChimeraX-SchemeMgr 1.0 Toolshed: register bundle ChimeraX-ToQuest 1.0 Toolshed: register bundle ChimeraX-MCopy 1.0 Toolshed: delay_registration mcopy Toolshed: register bundle ChimeraX-SmoothLines 1.0 Toolshed: delay_registration smoothlines Toolshed: register bundle ChimeraX-AmberInfo 1.0 Toolshed: register bundle ChimeraX-Segment 1.0.1 Toolshed: delay_registration segmentation Toolshed: register bundle ChimeraX-AtomSearch 2.0.1 Toolshed: register bundle ChimeraX-RotamerLibsDynameomics 2.0 Toolshed: register bundle ChimeraX-Shape 1.0.1 Toolshed: delay_registration shape boxPath Toolshed: delay_registration shape cone Toolshed: delay_registration shape cylinder Toolshed: delay_registration shape ellipsoid Toolshed: delay_registration shape icosahedron Toolshed: delay_registration shape rectangle Toolshed: delay_registration shape ribbon Toolshed: delay_registration shape sphere Toolshed: delay_registration shape triangle Toolshed: delay_registration shape tube Toolshed: register bundle ChimeraX-Dssp 2.0 Toolshed: register bundle ChimeraX-RotamerLibsDunbrack 2.0 Toolshed: register bundle ChimeraX-Struts 1.0.1 Toolshed: delay_registration struts Toolshed: delay_registration ~struts Toolshed: register bundle ChimeraX-SpaceNavigator 1.0 Toolshed: delay_registration device snav Toolshed: register bundle ChimeraX-IMOD 1.0 Toolshed: register bundle ChimeraX-RotamerLibsRichardson 2.0 Toolshed: register bundle ChimeraX-DataFormats 1.2.3 Toolshed: register bundle ChimeraX-Graphics 1.4.1 Toolshed: register bundle ChimeraX-Crystal 1.0 Toolshed: register bundle ChimeraX-ConnectStructure 2.0.1 Toolshed: register bundle ChimeraX-MouseModes 1.2 Toolshed: delay_registration ui mousemode Toolshed: delay_registration mousemode Toolshed: register bundle ChimeraX-Vive 1.1 Toolshed: delay_registration vr Toolshed: delay_registration xr Toolshed: delay_registration device vr Toolshed: register bundle ChimeraX-MapData 2.0 Toolshed: register bundle ChimeraX-WebCam 1.0.2 Toolshed: delay_registration webcam Toolshed: delay_registration device webcam Toolshed: register bundle ChimeraX-LookingGlass 1.1 Toolshed: delay_registration lookingglass Toolshed: delay_registration device lookingglass Toolshed: register bundle ChimeraX-vrml 1.0 Toolshed: register bundle ChimeraX-LinuxSupport 1.0.1 Toolshed: delay_registration linux xdg-install Toolshed: delay_registration linux xdg-uninstall Toolshed: delay_registration linux flatpak-files Toolshed: register bundle ChimeraX-EMDB-SFF 1.0 Toolshed: register bundle ChimeraX-Shortcuts 1.2.0 Toolshed: delay_registration ks Toolshed: delay_registration snapshot Toolshed: register bundle ChimeraX-AlphaFold 1.0.1 Toolshed: delay_registration alphafold match Toolshed: delay_registration alphafold fetch Toolshed: delay_registration alphafold search Toolshed: delay_registration alphafold predict Toolshed: delay_registration alphafold pae Toolshed: delay_registration alphafold contacts Toolshed: delay_registration alphafold dimers Toolshed: delay_registration alphafold monomers Toolshed: delay_registration alphafold interfaces Toolshed: register bundle ChimeraX-SideView 1.0.1 Toolshed: register bundle ChimeraX-Mask 1.0.2 Toolshed: delay_registration volume mask Toolshed: delay_registration volume onesmask Toolshed: register bundle ChimeraX-ColorKey 1.5.6 Toolshed: delay_registration key Toolshed: delay_registration ~key Toolshed: register bundle ChimeraX-CellPack 1.0 Toolshed: register bundle ChimeraX-BugReporter 1.0.1 Toolshed: register bundle ChimeraX-coulombic 1.4.4 Toolshed: delay_registration coulombic Toolshed: register bundle ChimeraX-TapeMeasure 1.0 Toolshed: register bundle ChimeraX-CheckWaters 1.4 Toolshed: register bundle ChimeraX-Map 1.3 Toolshed: delay_registration volume Toolshed: delay_registration molmap Toolshed: delay_registration measure mapstats Toolshed: delay_registration measure mapvalues Toolshed: register bundle ChimeraX-Log 1.2 Toolshed: delay_registration echo Toolshed: delay_registration log Toolshed: register bundle ChimeraX-SwapRes 2.5 Toolshed: delay_registration swapaa Toolshed: delay_registration swapna Toolshed: register bundle ChimeraX-OrthoPick 1.0.1 Toolshed: register bundle ChimeraX-UI 1.41 Toolshed: delay_registration ui Toolshed: delay_registration tool Toolshed: register bundle ChimeraX-HKCage 1.3 Toolshed: delay_registration hkcage Toolshed: register bundle ChimeraX-IHM 1.1 Toolshed: register bundle ChimeraX-BasicActions 1.1.2 Toolshed: delay_registration name Toolshed: delay_registration name frozen Toolshed: delay_registration name delete Toolshed: delay_registration name list Toolshed: register bundle ChimeraX-PDBLibrary 1.0.4 Toolshed: register bundle ChimeraX-Morph 1.0.2 Toolshed: delay_registration morph Toolshed: register bundle ChimeraX-Crosslinks 1.0 Toolshed: delay_registration crosslinks Toolshed: register bundle ChimeraX-AddCharge 1.5.18 Toolshed: delay_registration addcharge Toolshed: delay_registration addcharge nonstd Toolshed: register bundle ChimeraX-ModelPanel 1.5 Toolshed: register bundle ChimeraX-AlignmentHdrs 3.5 Toolshed: register bundle ChimeraX-Alignments 2.16.1 Toolshed: delay_registration sequence Toolshed: register bundle ChimeraX-Bumps 1.0 Toolshed: delay_registration bumps Toolshed: delay_registration cbumps Toolshed: register bundle ChimeraX-ItemsInspection 1.0.1 Toolshed: register bundle ChimeraX-Neuron 1.0 Toolshed: register bundle ChimeraX-Smiles 2.1.2 Toolshed: register bundle ChimeraX-OpenCommand 1.14 Toolshed: delay_registration open Toolshed: delay_registration usage open Toolshed: register bundle ChimeraX-Modeller 1.5.18 Toolshed: delay_registration modeller comparative Toolshed: delay_registration modeller loops Toolshed: delay_registration modeller refine Toolshed: delay_registration modeller scores Toolshed: register bundle ChimeraX-MapEraser 1.0.1 Toolshed: delay_registration volume erase Toolshed: register bundle ChimeraX-Shell 1.0.1 Toolshed: register bundle ChimeraX-MapSeries 2.1.1 Toolshed: delay_registration vseries Toolshed: delay_registration measure motion Toolshed: register bundle ChimeraX-MedicalToolbar 1.1 Toolshed: register bundle ChimeraX-MatchMaker 2.1.6 Toolshed: delay_registration matchmaker Toolshed: delay_registration mmaker Toolshed: register bundle ChimeraX-ReadPbonds 1.0.1 Toolshed: register bundle ChimeraX-SeqView 2.14 Toolshed: register bundle ChimeraX-Contacts 1.0.1 Toolshed: delay_registration interfaces Toolshed: register bundle ChimeraX-StructMeasure 1.2.1 Toolshed: register bundle ChimeraX-Nucleotides 2.0.3 Toolshed: delay_registration nucleotides Toolshed: delay_registration ~nucleotides Toolshed: register bundle ChimeraX-STL 1.0.1 Toolshed: register bundle ChimeraX-FunctionKey 1.0.1 Toolshed: delay_registration ui functionkey Toolshed: delay_registration functionkey Toolshed: register bundle ChimeraX-FileHistory 1.0.1 Toolshed: register bundle ChimeraX-ModelArchive 1.0 Toolshed: delay_registration modelcif pae Toolshed: register bundle ChimeraX-ChangeChains 1.1 Toolshed: delay_registration changechains Toolshed: register bundle ChimeraX-MDcrds 2.7.2 Toolshed: register bundle ChimeraX-IUPAC 1.0 Toolshed: register bundle ChimeraX-MapFit 2.0 Toolshed: delay_registration fitmap Toolshed: register bundle ChimeraX-MLP 1.1.1 Toolshed: delay_registration mlp Toolshed: register bundle ChimeraX-Registration 1.1.2 Toolshed: delay_registration registration status Toolshed: delay_registration registration file Toolshed: register bundle ChimeraX-gltf 1.0 Toolshed: register bundle ChimeraX-TaskManager 1.0 Toolshed: delay_registration taskman Toolshed: register bundle ChimeraX-Markers 1.0.1 Toolshed: delay_registration marker Toolshed: register bundle ChimeraX-BlastProtein 3.0.0 Toolshed: delay_registration blastprotein Toolshed: delay_registration blastpdb Toolshed: delay_registration blastprotein pull Toolshed: register bundle ChimeraX-BILD 1.0 Toolshed: register bundle ChimeraX-ButtonPanel 1.0.1 Toolshed: delay_registration buttonpanel Toolshed: register bundle ChimeraX-UnitCell 1.0.1 Toolshed: delay_registration unitcell Toolshed: register bundle ChimeraX-ColorActions 1.0.5 Toolshed: register bundle ChimeraX-PDB 2.7.6 Toolshed: register bundle ChimeraX-MapFilter 2.0.1 Toolshed: delay_registration volume add Toolshed: delay_registration volume bin Toolshed: delay_registration volume boxes Toolshed: delay_registration volume copy Toolshed: delay_registration volume cover Toolshed: delay_registration volume falloff Toolshed: delay_registration volume flatten Toolshed: delay_registration volume flip Toolshed: delay_registration volume fourier Toolshed: delay_registration volume gaussian Toolshed: delay_registration volume laplacian Toolshed: delay_registration volume localCorrelation Toolshed: delay_registration volume maximum Toolshed: delay_registration volume minimum Toolshed: delay_registration volume median Toolshed: delay_registration volume morph Toolshed: delay_registration volume multiply Toolshed: delay_registration volume new Toolshed: delay_registration volume octant Toolshed: delay_registration volume ~octant Toolshed: delay_registration volume permuteAxes Toolshed: delay_registration volume resample Toolshed: delay_registration volume ridges Toolshed: delay_registration volume scale Toolshed: delay_registration volume sharpen Toolshed: delay_registration volume subtract Toolshed: delay_registration volume threshold Toolshed: delay_registration volume tile Toolshed: delay_registration volume unbend Toolshed: delay_registration volume unroll Toolshed: delay_registration volume zone Toolshed: delay_registration volume unzone Toolshed: delay_registration vop Toolshed: register bundle ChimeraX-ResidueFit 1.0.1 Toolshed: delay_registration resfit Toolshed: register bundle ChimeraX-ImageFormats 1.2 Toolshed: register bundle ChimeraX-mmCIF 2.14.2 Toolshed: register bundle ChimeraX-Hbonds 2.5 Toolshed: delay_registration hbonds Toolshed: delay_registration ~hbonds Toolshed: register bundle ChimeraX-BuildStructure 2.13.1 Toolshed: delay_registration build Toolshed: delay_registration bond Toolshed: delay_registration ~bond Toolshed: delay_registration bond length Toolshed: register bundle ChimeraX-Surface 1.0.1 Toolshed: delay_registration color electrostatic Toolshed: delay_registration color sample Toolshed: delay_registration color gradient Toolshed: delay_registration color radial Toolshed: delay_registration color cylindrical Toolshed: delay_registration color height Toolshed: delay_registration color image Toolshed: delay_registration surface Toolshed: delay_registration ~surface Toolshed: delay_registration surface showPatches Toolshed: delay_registration surface hidePatches Toolshed: delay_registration surface close Toolshed: delay_registration surface style Toolshed: delay_registration surface squaremesh Toolshed: delay_registration surface showall Toolshed: delay_registration surface cap Toolshed: delay_registration surface dust Toolshed: delay_registration surface undust Toolshed: delay_registration surface hidefarblobs Toolshed: delay_registration surface invertShown Toolshed: delay_registration surface transform Toolshed: delay_registration surface zone Toolshed: delay_registration surface unzone Toolshed: delay_registration surface check Toolshed: delay_registration surface splitbycolor Toolshed: delay_registration sop Toolshed: delay_registration volume splitbyzone Toolshed: delay_registration measure sasa Toolshed: delay_registration measure volume Toolshed: delay_registration measure area Toolshed: delay_registration measure contactArea Toolshed: register bundle ChimeraX-CageBuilder 1.0.1 Toolshed: delay_registration cage Toolshed: register bundle ChimeraX-ViewDockX 1.4.4 Toolshed: delay_registration viewdockx Toolshed: delay_registration viewdockx down Toolshed: delay_registration viewdockx up Toolshed: register bundle ChimeraX-MutationScores 1.0 Toolshed: delay_registration mutationscores label Toolshed: delay_registration mutationscores define Toolshed: delay_registration mutationscores undefine Toolshed: delay_registration mutationscores scatterplot Toolshed: delay_registration mutationscores statistics Toolshed: delay_registration mutationscores histogram Toolshed: delay_registration mutationscores umap Toolshed: delay_registration mutationscores list Toolshed: delay_registration mutationscores structure Toolshed: delay_registration mutationscores close Toolshed: register bundle ChimeraX-RenumberResidues 1.1 Toolshed: delay_registration renumber Toolshed: register bundle ChimeraX-ShowSequences 1.0.3 Toolshed: register bundle ChimeraX-PubChem 2.2 Toolshed: register bundle ChimeraX-SwapAA 2.0.1 Toolshed: delay_registration swapaa mousemode Toolshed: register bundle ChimeraX-Nifti 1.2 Toolshed: register bundle ChimeraX-CrystalContacts 1.0.1 Toolshed: delay_registration crystalcontacts Toolshed: register bundle ChimeraX-ESMFold 1.0 Toolshed: delay_registration esmfold contacts Toolshed: delay_registration esmfold fetch Toolshed: delay_registration esmfold match Toolshed: delay_registration esmfold pae Toolshed: delay_registration esmfold predict Toolshed: delay_registration esmfold search Toolshed: register bundle ChimeraX-Label 1.1.14 Toolshed: delay_registration 2dlabels Toolshed: delay_registration scalebar Toolshed: delay_registration label Toolshed: delay_registration ~label Toolshed: register bundle ChimeraX-Mol2 2.0.3 Toolshed: register bundle ChimeraX-PickBlobs 1.0.1 Toolshed: delay_registration measure blob Toolshed: register bundle ChimeraX-NMRSTAR 1.0.2 Toolshed: register bundle ChimeraX-Mole 1.0 Toolshed: register bundle ChimeraX-Dicom 1.2.6 Toolshed: register bundle ChimeraX-BondRot 2.0.4 Toolshed: delay_registration torsion Toolshed: register bundle ChimeraX-Segger 1.0 Toolshed: delay_registration segger Toolshed: register bundle ChimeraX-Topography 1.0 Toolshed: delay_registration topography Toolshed: register bundle ChimeraX-PDBMatrices 1.0 Toolshed: register bundle ChimeraX-Help 1.3 Toolshed: delay_registration help Toolshed: register bundle ChimeraX-SDF 2.0.2 Toolshed: register bundle ChimeraX-AltlocExplorer 1.1.2 Toolshed: register bundle ChimeraX-SelInspector 1.0 Toolshed: register bundle ChimeraX-AlignmentMatrices 2.1 Toolshed: register bundle ChimeraX-Clashes 2.3 Toolshed: delay_registration clashes Toolshed: delay_registration contacts Toolshed: delay_registration ~clashes Toolshed: delay_registration ~contacts Toolshed: register bundle ChimeraX-WavefrontOBJ 1.0 Toolshed: register bundle ChimeraX-DistMonitor 1.4.2 Toolshed: delay_registration distance Toolshed: delay_registration ~distance Toolshed: register bundle ChimeraX-NRRD 1.2 Toolshed: register bundle ChimeraX-VTK 1.0 Toolshed: register bundle ChimeraX-Centroids 1.4 Toolshed: delay_registration define centroid Toolshed: register bundle ChimeraX-Storm 1.0 Toolshed: register bundle ChimeraX-CommandLine 1.2.5 Toolshed: register bundle ChimeraX-MMTF 2.2 Toolshed: register bundle ChimeraX-ChemGroup 2.0.1 Toolshed: register bundle ChimeraX-Atomic 1.58.8 Toolshed: delay_registration log chains Toolshed: delay_registration combine Toolshed: delay_registration pbond Toolshed: delay_registration ~pbond Toolshed: delay_registration label missing Toolshed: register bundle ChimeraX-Zone 1.0.1 Toolshed: delay_registration zone Toolshed: register bundle ChimeraX-VolumeMenu 1.0.1 Toolshed: register bundle ChimeraX-KVFinder 1.2.1 Toolshed: delay_registration kvfinder Toolshed: register bundle ChimeraX-uniprot 2.3.1 Toolshed: register bundle ChimeraX-Positions 1.0 Toolshed: register bundle ChimeraX-Tug 1.0.1 Toolshed: delay_registration tug Toolshed: register bundle ChimeraX-SaveCommand 1.5.1 Toolshed: delay_registration save Toolshed: delay_registration usage save Toolshed: register bundle ChimeraX-Toolbar 1.2.3 Toolshed: register bundle ChimeraX-AlignmentAlgorithms 2.0.2 Toolshed: register bundle ChimeraX-DockPrep 1.1.3 Toolshed: delay_registration dockprep Toolshed: register bundle ChimeraX-ModelSeries 1.0.1 Toolshed: delay_registration mseries Toolshed: register bundle ChimeraX-PDBBio 1.0.1 Toolshed: register bundle ChimeraX-AxesPlanes 2.4 Toolshed: delay_registration define plane Toolshed: delay_registration define axis Toolshed: register bundle ChimeraX-StdCommands 1.18.1 Toolshed: delay_registration alias Toolshed: delay_registration alias list Toolshed: delay_registration alias delete Toolshed: delay_registration ~alias Toolshed: delay_registration align Toolshed: delay_registration altlocs Toolshed: delay_registration angle Toolshed: delay_registration camera Toolshed: delay_registration cartoon Toolshed: delay_registration ~cartoon Toolshed: delay_registration cd Toolshed: delay_registration clip Toolshed: delay_registration ~clip Toolshed: delay_registration close Toolshed: delay_registration cofr Toolshed: delay_registration ~cofr Toolshed: delay_registration color Toolshed: delay_registration colour Toolshed: delay_registration color delete Toolshed: delay_registration color list Toolshed: delay_registration color name Toolshed: delay_registration color show Toolshed: delay_registration colordef Toolshed: delay_registration ~colordef Toolshed: delay_registration colourdef Toolshed: delay_registration ~colourdef Toolshed: delay_registration coordset Toolshed: delay_registration crossfade Toolshed: delay_registration defattr Toolshed: delay_registration delete Toolshed: delay_registration dssp Toolshed: delay_registration exit Toolshed: delay_registration quit Toolshed: delay_registration fly Toolshed: delay_registration getcrd Toolshed: delay_registration graphics Toolshed: delay_registration hide Toolshed: delay_registration ~show Toolshed: delay_registration ~display Toolshed: delay_registration lighting Toolshed: delay_registration lighting model Toolshed: delay_registration material Toolshed: delay_registration measure buriedarea Toolshed: delay_registration measure center Toolshed: delay_registration measure convexity Toolshed: delay_registration measure correlation Toolshed: delay_registration measure inertia Toolshed: delay_registration measure length Toolshed: delay_registration measure rotation Toolshed: delay_registration measure symmetry Toolshed: delay_registration measure weight Toolshed: delay_registration move Toolshed: delay_registration move cofr Toolshed: delay_registration palette Toolshed: delay_registration perframe Toolshed: delay_registration ~perframe Toolshed: delay_registration pwd Toolshed: delay_registration rainbow Toolshed: delay_registration rename Toolshed: delay_registration ribbon Toolshed: delay_registration ~ribbon Toolshed: delay_registration rmsd Toolshed: delay_registration rock Toolshed: delay_registration roll Toolshed: delay_registration runscript Toolshed: delay_registration select Toolshed: delay_registration ~select Toolshed: delay_registration set Toolshed: delay_registration ~set Toolshed: delay_registration setattr Toolshed: delay_registration show Toolshed: delay_registration display Toolshed: delay_registration size Toolshed: delay_registration split Toolshed: delay_registration stop Toolshed: delay_registration style Toolshed: delay_registration sym Toolshed: delay_registration tile Toolshed: delay_registration ~tile Toolshed: delay_registration time Toolshed: delay_registration transparency Toolshed: delay_registration turn Toolshed: delay_registration undo Toolshed: delay_registration redo Toolshed: delay_registration usage Toolshed: delay_registration version Toolshed: delay_registration view Toolshed: delay_registration wait Toolshed: delay_registration windowsize Toolshed: delay_registration wobble Toolshed: delay_registration worm Toolshed: delay_registration ~worm Toolshed: delay_registration select zone Toolshed: delay_registration zoom Toolshed: register bundle ChimeraX-Maestro 1.9.1 Toolshed: register bundle ChimeraX-AddH 2.2.6 Toolshed: delay_registration addh Toolshed: register bundle ChimeraX-ColorGlobe 1.0 Toolshed: register bundle ChimeraX-Meeting 1.0.1 Toolshed: delay_registration meeting start Toolshed: delay_registration meeting join Toolshed: delay_registration meeting Toolshed: delay_registration meeting close Toolshed: delay_registration meeting info Toolshed: delay_registration meeting settings Toolshed: delay_registration meeting server Toolshed: delay_registration meeting unname Toolshed: delay_registration meeting send Toolshed: register bundle ChimeraX-RenderByAttr 1.6.2 Toolshed: register bundle ChimeraX-RNALayout 1.0 Toolshed: delay_registration rna path Toolshed: delay_registration rna model Toolshed: register bundle ChimeraX-VIPERdb 1.0 Toolshed: register bundle ChimeraX-CoreFormats 1.2 Toolshed: register bundle ChimeraX-Segmentations 3.5.6 Toolshed: delay_registration ui view Toolshed: delay_registration segmentations Toolshed: Initiated toolshed check: 2025-02-06T12:19:31.798842 Toolshed: finished loading bundles NOTE: Initializing bundles Toolshed: initialize_bundles False Toolshed: initialize manager presets for bundle 'ChimeraX-PresetMgr' Toolshed: initialize manager rotamers for bundle 'ChimeraX-RotamerLibMgr' Toolshed: initialize manager url_schemes for bundle 'ChimeraX-SchemeMgr' Toolshed: initialize manager data formats for bundle 'ChimeraX-DataFormats' Toolshed: initialize manager alignments for bundle 'ChimeraX-Alignments' Toolshed: initialize manager items inspection for bundle 'ChimeraX-ItemsInspection' Toolshed: find_bundle ChimeraX-DataFormats True None Toolshed: initialize manager open command for bundle 'ChimeraX-OpenCommand' Toolshed: skip non-autostart manager start structure for bundle 'ChimeraX-BuildStructure' Toolshed: skip non-autostart manager start structure fragments for bundle 'ChimeraX-BuildStructure' Toolshed: skip non-autostart manager sequence features for bundle 'ChimeraX-Atomic' Toolshed: find_bundle ChimeraX-DataFormats True None Toolshed: initialize manager save command for bundle 'ChimeraX-SaveCommand' Toolshed: initialize manager toolbar for bundle 'ChimeraX-Toolbar' Toolshed: find_bundle ChimeraX-Toolbar True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Nucleotides True None Toolshed: find_bundle ChimeraX-Nucleotides True None Toolshed: find_bundle ChimeraX-Nucleotides True None Toolshed: find_bundle ChimeraX-Nucleotides True None Toolshed: find_bundle ChimeraX-Nucleotides True None Toolshed: skip non-autostart manager render by attribute for bundle 'ChimeraX-RenderByAttr' Toolshed: custom initialization for bundle 'ChimeraX-ToolshedUtils' Toolshed: custom initialization for bundle 'ChimeraX-RestServer' Toolshed: custom initialization for bundle 'ChimeraX-MouseModes' Toolshed: custom initialization for bundle 'ChimeraX-Vive' Toolshed: custom initialization for bundle 'ChimeraX-BugReporter' Toolshed: custom initialization for bundle 'ChimeraX-TapeMeasure' Toolshed: custom initialization for bundle 'ChimeraX-Map' Toolshed: custom initialization for bundle 'ChimeraX-Log' Toolshed: custom initialization for bundle 'ChimeraX-SwapRes' Toolshed: custom initialization for bundle 'ChimeraX-OrthoPick' Toolshed: custom initialization for bundle 'ChimeraX-BasicActions' Toolshed: custom initialization for bundle 'ChimeraX-MapEraser' Toolshed: custom initialization for bundle 'ChimeraX-MapSeries' Toolshed: custom initialization for bundle 'ChimeraX-StructMeasure' Toolshed: custom initialization for bundle 'ChimeraX-FunctionKey' Toolshed: custom initialization for bundle 'ChimeraX-Registration' Toolshed: custom initialization for bundle 'ChimeraX-Markers' Toolshed: custom initialization for bundle 'ChimeraX-BuildStructure' Toolshed: custom initialization for bundle 'ChimeraX-Surface' Toolshed: custom initialization for bundle 'ChimeraX-ViewDockX' Toolshed: custom initialization for bundle 'ChimeraX-SwapAA' Toolshed: custom initialization for bundle 'ChimeraX-Label' Toolshed: custom initialization for bundle 'ChimeraX-PickBlobs' Toolshed: custom initialization for bundle 'ChimeraX-NMRSTAR' Toolshed: custom initialization for bundle 'ChimeraX-Dicom' Toolshed: custom initialization for bundle 'ChimeraX-BondRot' Toolshed: custom initialization for bundle 'ChimeraX-Help' Toolshed: custom initialization for bundle 'ChimeraX-DistMonitor' Toolshed: custom initialization for bundle 'ChimeraX-CommandLine' Toolshed: custom initialization for bundle 'ChimeraX-ChemGroup' Toolshed: custom initialization for bundle 'ChimeraX-Atomic' Toolshed: custom initialization for bundle 'ChimeraX-Zone' Toolshed: custom initialization for bundle 'ChimeraX-VolumeMenu' Toolshed: custom initialization for bundle 'ChimeraX-Tug' Toolshed: custom initialization for bundle 'ChimeraX-StdCommands' Toolshed: custom initialization for bundle 'ChimeraX-Segmentations' Starting main interface Toolshed: find_bundle ChimeraX-Toolbar True None Toolshed: find_bundle ChimeraX-Toolbar True None Toolshed: find_bundle ChimeraX-Toolbar True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-SelInspector True None Toolshed: AvailableBundleCache.load: toolshed_url https://cxtoolshed.rbvi.ucsf.edu Toolshed: AvailableBundleCache.load: url https://cxtoolshed.rbvi.ucsf.edu/bundle/?uuid=773cf03f-db23-5226-968d-1f624be4b082&format_version=2 Toolshed: find_bundle ChimeraX-Core True None malloc(): unsorted double linked list corrupted Aborted (core dumped) jobilinux@SCMB-2DN9BY3:~$