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Opened 16 months ago
Last modified 16 months ago
#15596 assigned defect
Toolshed can't find ArtiaX bundle
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | high | Milestone: | |
| Component: | Tool Shed | Version: | |
| Keywords: | Cc: | chimera-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.2-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
ArtiaX bundle not available in v1.8 or daily build (from 11 July 2024):
"ArtiaX does not match any bundles"
Bundle is available in ChimeraX v1.7
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> toolshed reload available
> toolshed install ArtiaX
ArtiaX does not match any bundles
> toolshed install ChimeraX_ArtiaX-VERSION-py3-none-any.whl
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/toolshed.py", line 312, in toolshed_install
ts.install_bundle(bundles, logger, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 931, in install_bundle
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolshed_utils/__init__.py", line 216, in _install_bundle
raise ValueError("Non-existent wheel file")
ValueError: Non-existent wheel file
ValueError: Non-existent wheel file
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolshed_utils/__init__.py", line 216, in _install_bundle
raise ValueError("Non-existent wheel file")
See log for complete Python traceback.
> open /Volumes/villalab-
> rw/Projects/Josh/huabin_chromatin/batch/awi_v1/s109/s109_scene.cxc format
> cmd
> artiax start
Unknown command: artiax start
> toolshed install ArtiaX
ArtiaX does not match any bundles
> toolshed list full
List of installed bundles:
<string>:7: (WARNING/2) Definition list ends without a blank line; unexpected
unindent.
* AddCharge (1.5.17): Add partial charges to atoms
Category: Structure Editing
Add partial charges to atoms
Tool:
---
Add Charges | Add partial charges to structure
Commands:
addcharge | Add charges
addcharge nonstd | Add charges to non-standard residues
* AddH (2.2.6): Add hydrogens
Category: Structure Editing
Add hydrogens, using steric criteria and optionally H-bonds
Tool:
---
Add Hydrogens | Add hydrogens to structure
Command:
addh | Add hydrogens
* AlignmentAlgorithms (2.0.2): Sequence alignment algorithms
Category: Sequence alignment
This bundle provides a collection of sequence alignment algorithms.
* AlignmentHdrs (3.5): Alignment header support
Category: Sequence
Default useful alignment headers, and support for creating custom headers
* AlignmentMatrices (2.1): Sequence alignment similarity matrices
Category: Sequence alignment
Provide common sequence alignment BLOSUM similarity matrices.
* Alignments (2.12.7): Sequence alignment support
Category: Sequence
Sequence alignment support
Command:
---
sequence | control/open sequence alignments
* AlphaFold (1.0): Predict or fetch AlphaFold structures
Category: Structure Prediction
Predict structures using AlphaFold or fetch structures from the EBI AlphaFold
database
Tools:
---
AlphaFold | Fetch or calculate AlphaFold structures
AlphaFold Error Plot | Plot AlphaFold predicted aligned error
Commands:
alphafold match | Fetch AlphaFold database models matching a structure
alphafold fetch | Fetch AlphaFold database models for a UniProt identifier
alphafold search | Search AlphaFold database using BLAST
alphafold predict | Predict a structure using AlphaFold
alphafold pae | Show AlphaFold predicted aligned error as heatmap
alphafold contacts | Show AlphaFold contact pseudobond colored by predicted aligned error
alphafold dimers | Setup AlphaFold dimer predictions
alphafold monomers | Estimate time for AlphaFold predictions
alphafold interfaces | Evaluate AlphaFold PAE scores at dimer interfaces
* AltlocExplorer (1.1.1): Examine/change alternate atomic locations
Category: Structure Analysis
High-resolution structures may have several different possible positions for
an atom. ChimeraX only depicts one position for an atom. This tool allows the
user to determine which atoms have alternate locations and to change the
depiction to those locations if desired.
Tool:
---
Altloc Explorer | interact with alternate atom locations
* AmberInfo (1.0): Provide information about AmberTools installation
Category: Structure Editing
Provide information about AmberTools installation
* Arrays (1.1): C++ library for parsing numpy arrays
Category: Utility
C++ library for parsing numpy arrays passed from Python to C++ modules.
* Atomic (1.57.1): Atomic-structure functionality
Categories: Structure Analysis and Structure Editing
Python support for handling atomic structures
Commands:
---
log chains | show chain info in log
combine | copy or combine structure models
pbond | create a pseudobond
~pbond | delete a pseudobond
Selectors:
C1 | sp-hybridized carbon bonded to 2 other atoms
C1- | sp-hybridized carbon bonded to 1 other atom
C2 | sp2-hybridized carbon
C3 | sp3-hybridized carbon
Cac | carboxylate carbon
Car | aromatic carbon
D | other deuterium
DC | deuterium bonded to carbon
H | H (element)
HC | hydrogen bonded to carbon
N1 | sp-hybridized nitrogen bonded to 1 other atom
N1+ | sp-hybridized nitrogen bonded to 2 other atoms
N2 | sp2-hybridized nitrogen, double bonded
N2+ | sp2-hybridized nitrogen, double bonded, formal positive charge
N3 | sp3-hybridized nitrogen, neutral
N3+ | sp3-hybridized nitrogen, formal positive charge
Ng+ | guanidinium/amidinium nitrogen, partial positive charge
Npl | sp2-hybridized nitrogen, not double bonded
Ntr | nitro nitrogen
O1 | sp-hybridized oxygen
O1+ | sp-hybridized oxygen, formal positive charge
O2 | sp2-hybridized oxygen
O2- | carboxylate oxygen sharing formal negative charge; nitro group oxygen
O3 | sp3-hybridized oxygen
O3- | phosphate or sulfate oxygen sharing formal negative charge
Oar | aromatic oxygen
Oar+ | aromatic oxygen, formal positive charge
P3+ | sp3-hybridized phosphorus, formal positive charge
Pac | phosphate phosphorus
Pox | P-oxide phosphorus
S2 | sp2-hybridized sulfur
S3 | sp3-hybridized sulfur, neutral
S3+ | sp3-hybridized sulfur, formal positive charge
S3- | thiophosphate sulfur, sharing formal negative charge
Sac | sulfate, sulfonate, or sulfamate sulfur
Sar | aromatic sulfur
Son | sulfone sulfur
Sxd | sulfoxide sulfur
He | He (element)
Li | Li (element)
Be | Be (element)
B | B (element)
C | C (element)
N | N (element)
O | O (element)
F | F (element)
Ne | Ne (element)
Na | Na (element)
Mg | Mg (element)
Al | Al (element)
Si | Si (element)
P | P (element)
S | S (element)
Cl | Cl (element)
Ar | Ar (element)
K | K (element)
Ca | Ca (element)
Sc | Sc (element)
Ti | Ti (element)
V | V (element)
Cr | Cr (element)
Mn | Mn (element)
Fe | Fe (element)
Co | Co (element)
Ni | Ni (element)
Cu | Cu (element)
Zn | Zn (element)
Ga | Ga (element)
Ge | Ge (element)
As | As (element)
Se | Se (element)
Br | Br (element)
Kr | Kr (element)
Rb | Rb (element)
Sr | Sr (element)
Y | Y (element)
Zr | Zr (element)
Nb | Nb (element)
Mo | Mo (element)
Tc | Tc (element)
Ru | Ru (element)
Rh | Rh (element)
Pd | Pd (element)
Ag | Ag (element)
Cd | Cd (element)
In | In (element)
Sn | Sn (element)
Sb | Sb (element)
Te | Te (element)
I | I (element)
Xe | Xe (element)
Cs | Cs (element)
Ba | Ba (element)
La | La (element)
Ce | Ce (element)
Pr | Pr (element)
Nd | Nd (element)
Pm | Pm (element)
Sm | Sm (element)
Eu | Eu (element)
Gd | Gd (element)
Tb | Tb (element)
Dy | Dy (element)
Ho | Ho (element)
Er | Er (element)
Tm | Tm (element)
Yb | Yb (element)
Lu | Lu (element)
Hf | Hf (element)
Ta | Ta (element)
W | W (element)
Re | Re (element)
Os | Os (element)
Ir | Ir (element)
Pt | Pt (element)
Au | Au (element)
Hg | Hg (element)
Tl | Tl (element)
Pb | Pb (element)
Bi | Bi (element)
Po | Po (element)
At | At (element)
Rn | Rn (element)
Fr | Fr (element)
Ra | Ra (element)
Ac | Ac (element)
Th | Th (element)
Pa | Pa (element)
U | U (element)
Np | Np (element)
Pu | Pu (element)
Am | Am (element)
Cm | Cm (element)
Bk | Bk (element)
Cf | Cf (element)
Es | Es (element)
Fm | Fm (element)
Md | Md (element)
No | No (element)
Lr | Lr (element)
Rf | Rf (element)
Db | Db (element)
Sg | Sg (element)
Bh | Bh (element)
Hs | Hs (element)
Mt | Mt (element)
Ds | Ds (element)
Rg | Rg (element)
Cn | Cn (element)
Uut | Uut (element)
Fl | Fl (element)
Uup | Uup (element)
Uuh | Uuh (element)
Uus | Uus (element)
Uuo | Uuo (element)
backbone | backbone atoms
mainchain | backbone atoms
min-backbone | minimal backbone atoms
ions | ions
ligand | ligands
main | main structure
solvent | solvent
protein | proteins
nucleic | nucleic acids
nucleic-acid | nucleic acids
sel-residues | current selection promoted to full residues
strand | beta sheet strands
helix | protein helices
coil | protein coils
sidechain | side-chain atoms
sideonly | side-chain atoms
ribose | ribose
template-mismatch | residues whose heavy atoms don't match the residue template
* AtomicLibrary (14.0.6): Atomic-structure C++ library
Categories: Structure Analysis and Structure Editing
C++ support for handling atomic structures
* AtomSearch (2.0.1): 3D atom search
Category: Structure Analysis
Quickly search 3D space for atom within a certain distance of another atom or
a xyz point.
* AxesPlanes (2.4): Depict axes or planes
Category: Structure Analysis
Define and depict axes or planes, and make measurements involving them
Commands:
---
define plane | Create a plane in the scene
define axis | Create an axis in the scene
* BasicActions (1.1.2): Basic actions for user-defined specifier names
Category: General
Manager for user-defined specifier names.
Names are listed and may be used to display, hide or color associated atoms,
cartoons and surfaces.
Tool:
---
Basic Actions | show/hide atoms, ribbons and surfaces
Commands:
name | Define specifier name as a string
name frozen | Define specifier name as atoms in current session matching a string
name delete | Remove user-defined specifier name
name list | List user-defined specifier names
* BILD (1.0): BILD file reader
Category: Generic 3D objects
BILD is a simple text format that describes
lines, polygons, and geometric primitives such as spheres, boxes, cylinders, and cones with commands that was used in UCSF Chimera. Character strings can also be included. The objects can be specified in absolute coordinates and/or transformed and scaled coordinates.
* BlastProtein (2.4.6): Search PDB/NR/AlphaFold using BLAST
Category: Sequence
Interface to the RBVI web service to search the PDB, NR, or AlphaFold
databases using BLAST. Results are shown in a tool when a graphical interface
is available; otherwise, the results are logged.
Tool:
---
Blast Protein | Search PDB/NR/AlphaFold using BLAST
Commands:
blastprotein | Search PDB/NR/AlphaFold using BLAST
blastpdb | Search PDB/NR/AlphaFold using BLAST
blastprotein pull | Get results for a finished BlastProtein job
* BondRot (2.0.4): Bond rotation support
Category: Structure Editing
Bond rotation support
Command:
---
torsion | Report torsion angle of 4 atoms, or set it (middle two atoms must be bonded for setting)
* BugReporter (1.0.1): Report bugs when an error occurs
Category: General
Tool to allow sending a ChimeraX bug report when an error occurs.
* BuildStructure (2.12.1): Create/modify structures
Category: Structure Analysis
Create/modify atomic structures
Tool:
---
Build Structure | Create/modify structures
Commands:
build | Create/modify structures
bond | Create bond(s)
~bond | Remove bond(s)
bond length | change bond length(s)
* Bumps (1.0): Find protrusions in density maps
Category: Volume Data
Find protrusions of cells in light microscopy 3d images.
Commands:
---
bumps | find protrusions in density maps
cbumps | find convex surface patches
* ButtonPanel (1.0.1): Create custom user interface panels
Category: General
Create custom user interface panels with buttons that run specified commands.
Command:
---
buttonpanel | Create custom user interface panels
* CageBuilder (1.0.1): Build polygonal meshes for oligomeric molecular assemblies
Category: Higher-Order Structure
Cage Builder creates polyhedral cages composed of hexagons, pentagons, squares
and other polygons. The cages can be decorated with atomic models to create
oligomeric molecular assemblies.
Tool:
---
Cage Builder | Build polygonal meshes
Command:
cage | Place copies of model on polygons of cage
* CellPack (1.0): Fetch cellPACK models from web
Category: Molecular structure
The ChimeraX-CellPack bundle provides support fo reading cellPack data files
via the Internet. See http://www.cellpack.org for more information.
* Centroids (1.4): Depict centroid of atoms
Category: Structure Analysis
Depict centroid of atoms
Command:
---
define centroid | Depict centroid
* ChangeChains (1.1): Change chain IDs
Category: Structure Editing
Change chain IDs
Tool:
---
Change Chain IDs | change chain IDs
Command:
changechains | change chain IDs
* CheckWaters (1.4): Check water placement in maps
Category: Volume Data
Investigate water placement in volumetric maps
Tool:
---
Check Waters | Check water placement in a map
* ChemGroup (2.0.1): Detect chemically functional groups
Category: Structure Analysis
This bundle provides the ability for detection of functional groups in a
structure.
Selectors:
acyl-halide | R(C=O)X
adenine | 6-aminopurine
aldehyde | R(C=O)H
amide | R(C=O)NR2
amine | RxNHy
aliphatic-amine | RxNHy
aliphatic-primary-amine | RNH2
aliphatic-secondary-amine | R2NH
aliphatic-tertiary-amine | R3N
aliphatic-quaternary-amine | R4N+
aromatic-amine | RxNHy
aromatic-primary-amine | RNH2
aromatic-secondary-amine | R2NH
aromatic-tertiary-amine | R3N
aromatic-ring | aromatic
carbonyl | R2C=O
carboxylate | RCOO-
cytosine | 2-oxy-4-aminopyrimidine
disulfide | RSSR
ester | R(C=O)OR
ether-O | ROR
guanine | 2-amino-6-oxypurine
halide | RX
hydroxyl | COH or NOH
imine | R2C=NR
ketone | R2C=O
methyl | RCH3
nitrile | RC*N
nitro | RNO2
phosphate | PO4
phosphinyl | R2PO2-
phosphonate | RPO3-
purines | purine-like rings
pyrimidines | pyrimidine-like rings
sulfate | SO4
sulfonamide | RSO2NR2
sulfonate | RSO3-
sulfone | R2SO2
sulfonyl | R2SO2
thiocarbonyl | C=S
thioether | RSR
thiol | RSH
thymine | 5-methyl-2,4-dioxypyrimidine
uracil | 2,4-dioxypyrimidine
sulphate | SO4
sulphonamide | RSO2NR2
sulphonate | RSO3-
sulphone | R2SO2
sulphonyl | R2SO2
aromatic | aromatic
* Clashes (2.2.4): Find clashes/contacts in structures
Category: Structure Analysis
Find atomic clashes/contacts in structures
Tools:
---
Clashes | Find atom-atom clashes
Contacts | Find atom-atom contacts
Commands:
clashes | Find atoms with steric clashes
contacts | Finds atoms in contact with one another
~clashes | Clear clash pseudobond
~contacts | Clear contact pseudobond
* ColorActions (1.0.5): Simple interface for coloring objects
Category: Depiction
Simple interface for coloring atoms, bonds, surfaces, etc.
Tool:
---
Color Actions | color items
* ColorGlobe (1.0): Show directional resolution colored sphere
Category: General
Show directional resolution colored sphere.
* ColorKey (1.5.6): Add color key to graphics
Category: Depiction
Overlay color key on graphics scene.
Tool:
---
Color Key | add color key to graphics
Commands:
key | add color key to graphics
~key | remove color key
* CommandLine (1.2.5): Command line support
Category: General
Provide command line tool with command history.
Tool:
---
Command Line Interface | Command Line Interface
* ConnectStructure (2.0.1): Add bonds to structures that lack them
Category: Structure Analysis
Add bonds to structures based on inter-atomic distances
* Contacts (1.0.1): Display chain contact maps
Category: Molecular structure
Display chain contact maps.
Command:
---
interfaces | Display chain contact maps
* Core (1.8): ChimeraX Core Package
Category: Core
Missing bundle description
* CoreFormats (1.2): ChimeraX session support
Category: Atomic Data
ChimeraX session support
* coulombic (1.4.3): Compute/show electrostatic potential
Category: Surface/Binding Analysis
Compute and electrostatic potential according to Coulomb's law and either
create a corresponding volume (three-dimensional grid) or color a surface.
Command:
---
coulombic | Color surface based on electrostatics
* Crosslinks (1.0): Analyze crosslinks
Category: General
Plot or minimize crosslink lengths.
Command:
---
crosslinks | Plot or minimize crosslink lengths
* Crystal (1.0): Crystal symmetries
Category: Generic 3D objects
Provide matrices for crystallographic space groups.
* CrystalContacts (1.0.1): Show contacting asymmetric units in a crystal
Category: Higher-Order Structure
Makes copies of a crystal asymmetric unit for all contacting asymmetric units.
Tool:
---
Crystal Contacts | Show contacting subunits in a crystal
Command:
crystalcontacts | Make contacting copies of a crystal asymmetric unit
* DataFormats (1.2.3): Data format management
Category: Utilities
Manager for data format information
* Dicom (1.2.4): Read medical imaging and segmentations in DICOM format
Category: Medical Imaging
Read medical imaging and segmentations in DICOM format.
Tools:
---
DICOM Browser | View the metadata of a patient's DICOM files
Download DICOM | View the contents of public DICOM datasets from within ChimeraX
* DiffPlot (1.0): Cluster structures by conformation
Category: Molecular structure
Cluster structures by conformation.
Command:
---
diffplot | Display UMAP plot of structure differences
* DistMonitor (1.4.2): Interactive distance display
Category: Structure Analysis
Support for showing interactive distances on pseudobonds
Commands:
---
distance | determine distance
~distance | remove distance monitors
* DockPrep (1.1.3): Prepare structures for docking
Category: Structure Editing
Prepare structures for docking (or other computations such as minimization) by
adding hydrogens, filling out missing side chains, etc.
Tool:
---
Dock Prep | prepare structures for docking
Command:
dockprep | prepare structures for docking
* Dssp (2.0): Compute/assign secondary structure
Category: Structure Analysis
Use Kabsch and Sander 'Define Secondary Structure of Proteins' algorithm to
compute and assign secondary structure. See
https://en.wikipedia.org/wiki/DSSP_(hydrogen_bond_estimation_algorithm)
* EMDB-SFF (1.0): EMDB SFF file reader
Category: Volume Data
Read segmentation files in EMDB SFF format.
* ESMFold (1.0): Predict or fetch ESMFold structures
Category: Structure Prediction
Predict structures using ESMFold or fetch them from the ESM Metagenomic Atlas
Tools:
---
ESMFold | Fetch or calculate ESMFold structures
ESMFold Error Plot | Plot ESMFold predicted aligned error
Commands:
esmfold contacts | Show ESMFold contact pseudobond colored by predicted aligned error
esmfold fetch | Fetch ESM Metagenomic Atlas models for a MGnify accession code
esmfold match | Fetch ESM Metagenomic Atlas models matching a structure
esmfold pae | Show ESMFold predicted aligned error as heatmap
esmfold predict | Predict a structure using ESMFold
esmfold search | Search ESMFold database using BLAST
* FileHistory (1.0.1): File History Panel
Category: General
Display thumbmails of the list of recently opened files in a panel.
Tool:
---
File History | Show recently opened files
* FunctionKey (1.0.1): Assign function keys to run commands
Category: General
Assign function keys to run commands
Commands:
---
ui functionkey | Assign function keys to run commands
functionkey | Assign function keys to run commands
* Geometry (1.3): Vector and coordinate system routines
Category: Utility
Routines for vectors, rotations, coordinate transformations, bounding boxes
and
miscellaneous 3D scene geometry calculations.
* gltf (1.0): Read/write glTF 3d scene files
Category: Generic 3D objects
Read and write glTF 3d scene files.
* Graphics (1.1.1): OpenGL graphics rendering
Category: Graphics
Render scenes using a camera, view and hierarchy of drawings.
* Hbonds (2.4): Identify hydrogen bonds in and among structures
Category: Structure Analysis
Identify hydrogen bonds in and among structures
Tool:
---
H-Bonds | Find hydrogen bonds
Commands:
hbonds | Find hydrogen bonds
~hbonds | Clear hydrogen bonds
* Help (1.2.2): Show ChimeraX Help
Category: Documentation
Support help command and GUI.
Command:
---
help | Display ChimeraX help
* HKCage (1.3): Create icosahedral mesh of hexagons and pentagons
Category: Higher-Order Structure
Create icosahedral mesh of hexagons and pentagons using h and k lattice
parameters.
Command:
---
hkcage | Create icosahedral cage
* IHM (1.1): Integrative Hybrid Models file reader
Category: Higher-Order Structure
Support Integrative Hybrid Models.
* ImageFormats (1.2): Support for saving images
Category: I/O
Support for saving images
* IMOD (1.0): IMOD model file reader
Category: Volume Data
Read meshes and contours from IMOD model files.
* IO (1.0.1): Python convenience input/output functions
Category: Input/Output
Python functions to more easily open files while allowing for comression, home
directory or environment variable expansion, etc.
* ItemsInspection (1.0.1): Inspection of attributes of a set of items
Category: General Controls
Infrastructure for generic inspection of a set of items (attributes/values)
* IUPAC (1.0): IUPAC fetch
Category: Molecular structure
This bundle provides the abiility to get 3D structures for IUPAC identifiers.
* Label (1.1.10): Add text labels to graphics
Category: General
Overlay 2D text on graphics scene.
Tool:
---
Scale Bar | Show a scale bar
Commands:
2dlabels | add text labels to graphics
scalebar | show a scalebar
label | add 3d labels to graphics
~label | remove 3d labels from graphics
* ListInfo (1.2.2): Report attributes for selected atomic data
Category: General
Report attributes for selected atomic data
Command:
---
info | Report attributes for models and atomic data
* Log (1.1.6): Log support
Category: General
The ChimeraX-Log bundle provides a tool for viewing a log of what the user has
done.
Tool:
---
Log | Log of information and output
Commands:
echo | Log a line of text
log | manipulate the Log tool
* LookingGlass (1.1): LookingGlass holographic display
Category: General
Show graphics on LookingGlass holographic display.
Commands:
---
lookingglass | Render to LookingGlass holographic display
device lookingglass | Render to LookingGlass holographic display
* Maestro (1.9.1): Maestro reader
Category: I/O
Schrodinger Maestro input.
* Map (1.2): Density maps
Category: Volume Data
Display and analyze 3d image data
Tools:
---
Volume Viewer | Show density maps info
Map Coordinates | Adjust density map coordinates
Map Statistics | Report map minimum, maximum, mean, standard deviation, and root mean square
Commands:
volume | control volume data display
molmap | create density map for molecule
measure mapstats | report map statistics
measure mapvalues | Intepolate map at atom positions
* MapData (2.0): Volume data file formats
Category: Volume Data
Open and save volume data.
* MapEraser (1.0.1): Map eraser
Category: Volume data
Erase image data within a sphere.
Tool:
---
Map Eraser | Erase part of a density map within a sphere
Command:
volume erase | Erase part of a density map within a sphere
* MapFilter (2.0.1): Operations on maps
Category: Volume Data
Volume subcommands that create a new map from an existing map
Tool:
---
Map Filter | Apply filters to maps
Commands:
volume add | Add two or more maps
volume bin | Average map values over bins to reduce map size
volume boxes | Extract maps for boxes around selected atoms
volume copy | Copy a map or a map subregion
volume cover | Use symmetry to extend a map to cover a region
volume falloff | Smooth map values where map falls to zero
volume flatten | Flatten map gradients
volume flip | Reverse axis directions
volume fourier | Fourier transform a map
volume gaussian | Convolve map with a Gaussian for smoothing
volume laplacian | Laplace filter a map to enhance edges
volume localCorrelation | Compute correlation between maps over a slid
volume maximum | Maximum pointwise values of 2 or more maps
volume minimum | Minimum pointwise values of 2 or more maps
volume median | Median map value over a sliding window
volume morph | Linearly interpolate maps
volume multiply | Multiply maps pointwise
volume new | Create a new map with zero values
volume octant | Zero all but an octant of a map
volume ~octant | Zero an octant of a map
volume permuteAxes | Permute map axes
volume resample | Resample a map on the grid of another map
volume ridges | Filter to detect map ridges
volume scale | Scale and shift map values
volume sharpen | Sharpen map by amplifying high-frequencies using bfactor
volume subtract | Subtract maps pointwise
volume threshold | Set map values below a threshold to zero
volume tile | Create a single plane map by tiling planes of a map
volume unbend | Unwarp a map along a curved rectangular tube
volume unroll | Unroll a cylindrical shell to form a new map
volume zone | Zero map values beyond a distance range from atoms
volume unzone | Show full map with no surface masking
vop | Synonym for volume command for backward compatibility with Chimera
* MapFit (2.0): Fit molecules into maps
Category: Volume Data
Rigid body motion of molecules and maps into other maps.
Tool:
---
Fit in Map | Fit molecules in maps
Command:
fitmap | fit molecules in maps
* MapSeries (2.1.1): Volume series
Category: Volume Data
Display and analyze 3d image time series.
Commands:
---
vseries | volume series
measure motion | volume series cactus prickles
* Markers (1.0.1): Place markers on density maps
Category: Volume Data
Mouse mode to place markers on density maps.
Tool:
---
Marker Placement | Place markers on density maps
Command:
marker | Place markers
* Mask (1.0.2): Mask a volume to a surface
Category: Volume Data
Copy a volume setting values outside a surface to zero
Commands:
---
volume mask | Mask a map to a surface
volume onesmask | Create a onesmask inside a surface
* MatchMaker (2.1.3): Superimpose structures
Category: Sequence
MatchMaker superimposes protein or nucleic acid structures by first creating
pairwise sequence alignments, then fitting the aligned residue pairs. Residue
types and/or secondary structure information can be used to create the initial
sequence alignments. Fitting uses one point per residue. Optionally, a
structure-based multiple sequence alignment can be computed after the
structures have been superimposed.
Tool:
---
Matchmaker | superimpose structures/chains
Commands:
matchmaker | Superimpose structures
mmaker | alias of matchmaker
* MCopy (1.0): Copy atomic structure attributes to another structure
Category: Molecular structure
Copy colors, styles, positions, ... of an atomic model to another atomic
model.
Command:
---
mcopy | Copy atomic structure display properties
* MDcrds (2.7.1): Molecular dynamics support
Category: Molecular Dynamics
This bundle provides parsers for various molecular dynamics file formats.
* MedicalToolbar (1.0.3): Toolbar for medical image analysis
Category: Toolbar
Provide a toolbar tab including buttons useful for medical image
visualization.
* Meeting (1.0.1): Shared interactive VR sessions.
Category: General
Show virtual reality hand controllers or mouse from ChimeraX running on a
remote machine.
Tool:
---
Meeting | Multi-person sessions
Commands:
meeting start | Create a ChimeraX meeting
meeting join | Join a ChimeraX meeting
meeting | Same as meeting join
meeting close | Close a ChimeraX meeting
meeting info | Report ChimeraX meeting info
meeting settings | Report or set meeting default settings
meeting server | Report or define meeting server names
meeting unname | Deregister a meeting name
meeting send | Copy my scene to all other meeting participants
* MLP (1.1.1): Molecular lipophilicity calculation
Category: Molecular structure
Molecular lipophilicity calculation
Based on:
> pyMLP Molecular Lipophilic Potential evaluator Copyright (c) 2006-2007
> Julien Lefeuvre <lefeuvrejulien@yahoo.fr>
>
> Software License Agreement (BSD-new License)
>
> Copyright (c) 2006-2015, Julien Lefeuvre <julien@lefeuv.re> Contributors: -
> Julien Lefeuvre <julien@lefeuv.re>
>
> All rights reserved.
Command:
---
mlp | Molecular lipophilicity calculation
* mmCIF (2.14.1): mmCIF format read/write
Category: Molecular structure
This bundle provides the abiility to fetch and read Macromolecular CIF files.
* MMTF (2.2): MMTF format read/write
Category: Molecular structure
This bundle provides the abiility to fetch and read MMTF files.
* Modeller (1.5.17): Interface to Modeller
Categories: Sequence and Structure Prediction
Perform comparitive or loop modeling.
Tools:
---
Modeller Comparative | Generate comparative models
Model Loops | Model/remodel structure segments
Commands:
modeller comparative | Generate comparative models
modeller loops | Fill missing structure
modeller refine | Fill missing structure
modeller scores | Fetch Modeller scores for a model
* ModelPanel (1.5): ChimeraX Model Panel
Category: General
ChimeraX Model Panel.
Tool:
---
Model Panel | model panel
* ModelSeries (1.0.1): Display sequences of models one by one
Category: General
Display sequences of models one by one.
Command:
---
mseries | Display sequence of models one by one
* Mol2 (2.0.3): Mol2 reader/writer
Category: I/O
Sybyl Mol2 input/output.
* Mole (1.0): Open JSON tunnel files from Mole
Category: Structure Analysis
Open JSON tunnel files from Mole
* Morph (1.0.2): Morph atomic structures
Category: Morph Structures
This bundle provides the morph command to smoothly interpolate between
different conformations of an atomic structure.
Command:
---
morph | morph atomic structures
* MouseModes (1.2): Provide right button mouse mode tool
Category: Toolbar
Provide a series of icons for changing the assigment of the right mouse
button.
Commands:
---
ui mousemode | set/list mouse modes
mousemode | set/list mouse modes
* Movie (1.0): Commands to record movies
Category: General
Provide commands for capturing images and assembling them into movies.
Command:
---
movie | record movies
* Neuron (1.0): Read SWC neuron trace files
Category: Generic 3D objects
Read SWC neuron trace files.
* Nifti (1.2): Read medical images in NIfTI format
Category: Volume Data
Read medical imaging and segmentations in NIfTI format.
* NMRSTAR (1.0.2): Read NMR distance restraints from NMR-STAR files
Category: Generic 3D objects
Read NMR distance restraints from NMR-STAR files.
* NRRD (1.2): Read medical images in NRRD format
Category: Volume Data
Read medical imaging and segmentations in NRRD format.
* Nucleotides (2.0.3): Create nucleotide-specific displays
Category: General
Create special nucleotide-specific displays of the base and sugar moieties.
Such displays are generally combined with various atomic representations
and/or cartoons.
See also
Nucleic acid visualization with UCSF Chimera.
System Message: WARNING/2 (`<string>`, line 7)
Definition list ends without a blank line; unexpected unindent.
Couch GS, Hendrix DK, Ferrin TE. Nucleic Acids Res. 2006 Feb 14;34(4):e29.
Commands:
---
nucleotides | Manipulate nucleotide representations
~nucleotides | Undo nucleotide representations
* OpenCommand (1.13.5): Manages 'open' command extensibility
Category: Commands
Handles 'open' command and manages bundles extending its capabilities
Commands:
---
open | Open/fetch data files
usage open | Show syntax of 'open' command
* PDB (2.7.5): PDB format read/write
Category: Molecular structure
This bundle provides the abiility to fetch and read PDB files.
* PDBBio (1.0.1): PDB biological assembly fetch
Category: Molecular structure
Fetch biological assembly models from the PDB database.
* PDBLibrary (1.0.4): C++ PDB support
Category: Molecular structure
This provides a PDB-related C++ library.
* PDBMatrices (1.0): Crystal and biological unit matrices
Category: Molecular structure
Extract crystal and biological unit matrices from mmCIF and PDB files.
* PickBlobs (1.0.1): Measure and color blobs
Category: Volume data
Measure and color connected parts of a surface.
Tool:
---
Measure and Color Blobs | Measure and color connected parts of surfaces
Command:
measure blob | Measure and color connected parts of surfaces
* Positions (1.0): Read and write model position matrices
Category: Generic 3D objects
Read and write model position matrices.
* PresetMgr (1.1.1): Preset management
Category: Depiction
Manager for preset information
Command:
---
preset | apply "preset" depiction to models
* PubChem (2.2): PubChem fetch
Category: Molecular structure
This bundle provides the abiility to fetch PubChem files.
* ReadPbonds (1.0.1): Read in pseudobonds from a file
Category: Generic 3D objects
Read in pseudobonds from a text file.
* Registration (1.1.2): Register ChimeraX
Category: Utilities
Register ChimeraX with RBVI and help us document the impact this software is
having in the scientific community. The information you supply will only be
used for reporting summary statistics to NIH.
Tool:
---
Registration | Register ChimeraX with RBVI
Commands:
registration status | Report registration status
registration file | Report registration file location or apply registration file
* RemoteControl (1.0): Control ChimeraX from other apps
Category: General
Provide the ability to send commands to ChimeraX from other applications.
Command:
---
remotecontrol xmlrpc | synopsis
* RenderByAttr (1.4.1): Depict attribute values on structures
Categories: Depiction and Structure Analysis
Depict attribute values on structures and surfaces using colors, atom sizes,
or cartoon thickness.
Tool:
---
Render/Select by Attribute | depict attribute values on structures
* RenumberResidues (1.1): Renumber residues
Category: Structure Editing
Renumber residues
Tool:
---
Renumber Residues | renumber residues
Command:
renumber | renumber residues
* ResidueFit (1.0.1): Display fit of residues to density map
Category: General
Display fit of residues to density map.
Command:
---
resfit | Display slider to show fit of each residue in density map
* RestServer (1.2): Starts REST server to execute commands from network requests
Category: General
Starts REST server to execute commands from network requests
Server is listening on a local port for HTTP requests. The request content is
executed as a ChimeraX command and the generated output is returned as the
response.
Command:
---
remotecontrol rest | Control REST server
* RNALayout (1.0): Make RNA models
Category: Structure Editing
Create RNA models from secondary structure information.
Commands:
---
rna path | make RNA marker model
rna model | make RNA atomic model
* RotamerLibMgr (4.0): Manage rotamer libraries
Category: Structure Editing
Manager for rotamer libraries (provided by other bundles)
* RotamerLibsDunbrack (2.0): Dunbrack rotamer library
Category: Structure Editing
Dunbrack 2010 backbone-dependent rotamer library -- 5% stepdown
* RotamerLibsDynameomics (2.0): Dynameomics rotamer library
Category: Structure Editing
Dynameomics backbone-independent rotamer library -- March '12
* RotamerLibsRichardson (2.0): Richardson rotamer libraries
Category: Structure Editing
Richardson lab backbone-independent rotamer libraries
* SaveCommand (1.5.1): Manages 'save' command extensibility
Category: Commands
Handles 'save' command and manages bundles extending its capabilities
Commands:
---
save | Save data files
usage save | Show 'save' command syntax
* SchemeMgr (1.0): HTTP scheme management
Category: Utilities
Manager for tracking HTTP schemes used in ChimeraX bundles
* SDF (2.0.2): SDF file reader
Category: Atomic Data
The ChimeraX-SDF bundle provides support for reading structures from MDL
SDF/MOL files
* Segger (1.0): Segment map
Category: Volume data
Segment density maps using Segger watershed methods.
Tools:
---
Segment Map | Segment density maps using Segger algorithms
Fit to Segments | Fit atomic models in segmented maps
Command:
segger | Operate on Segger segmentations
* Segment (1.0.1): Watershed segment calculation
Category: Volume data
Calculate watershed segmentation regions for density maps.
Command:
---
segmentation | color and surface segmentations
* Segmentations (3.0.15): Segment any volume data
Category: Volume Data
Segment any volume data
Tool:
---
Segmentations | Interactively segment volumes
Commands:
ui view | See medical images in a 4-panel viewer
segmentations | Create, edit, or destory segmentations
* SelInspector (1.0): Inspect contents of selection
Category: General Controls
Inspect/change attributes of current selection
Tool:
---
Selection Inspector | inspect selection contents
* SeqView (2.11.2): Sequence viewer
Category: Sequence
Sequence/alignment viewer.
* Shape (1.0.1): Make models for geometric shapes
Category: Generic 3D objects
Create geometric shapes like spheres, cylinders, cones, tubes, icosahedrons.
Commands:
---
shape boxPath | create a box beam model
shape cone | create a cone model
shape cylinder | create a cylinder model
shape ellipsoid | create an ellipsoid model
shape icosahedron | create a icosahedron model
shape rectangle | create a rectangle model
shape ribbon | create a ribbon model
shape sphere | create a sphere model
shape triangle | create a triangle model
shape tube | create a tube model
* Shell (1.0.1): Interactive Python shell
Category: General
Provide IPython interactive shell, https://ipython.org/ipython-
doc/3/interactive/qtconsole.html. The current ChimeraX session is available in
the global variable 'session'.
Tool:
---
Shell | Python shell
* Shortcuts (1.1.1): Button and keyboard shortcuts
Category: Toolbar
Provide button and keyboard shortcuts for common commands.
Commands:
---
ks | keyboard shortcuts
snapshot | Save graphics image
Selectors:
selAtoms | Selected atoms, or if none selected then all atoms.
selMaps | Selected maps, or if none selected then displayed maps.
selModels | Selected models, or if none selected then all models.
last-opened | Last opened top level model including its atoms.
* ShowSequences (1.0.3): Choose/show structure sequences
Category: Sequence
Simgle interface to bring up a sequence viewer for structure chains
Tool:
---
Show Sequence Viewer | show chain sequences
* SideView (1.0.1): Side view of scene
Category: General
Show camera settings (eye position and clipping planes) overlayed on the scene
and allow for them to be interactively changed.
Tool:
---
Side View | Show side view interface
* Smiles (2.1.2): SMILES fetch
Category: Molecular structure
This bundle provides the abiility to get 3D structures for SMILES strings.
* SmoothLines (1.0): Smooth network of lines
Category: General
Smooth network of lines.
Command:
---
smoothlines | Smooth networks of lines
* SpaceNavigator (1.0): Space Navigator device support
Category: General
This bundle allows using 3dconnexion space navigator devices to move models.
Command:
---
device snav | Control SpaceNavigator device
* StdCommands (1.16.5): Standard commands
Category: Structure Analysis
General purpose commands always available in ChimeraX
Commands:
---
alias | create shorthand version of command
alias list | list command aliases
alias delete | remove command alias
~alias | remove command alias
align | superimpose specific parts of structures
altlocs | change/remove alternate atom locations
angle | Report or set angle between atoms/objects
camera | change "camera" parametrs of main viewing window
cartoon | show stylized representation of structure
~cartoon | stop show stylized representation of structure
cd | change ChimeraX's current working directory
clip | control clipping of models
~clip | stop clipping of models
close | close models
cofr | set center of rotation
~cofr | revert to default center of rotation
color | change model colors
colour | change model colors
color delete | delete custom color names
color list | list custom color names
color name | define custom color names
color show | show definition of custom color names
colordef | define custom color names
~colordef | remove custom color names
colourdef | define custom color names
~colourdef | remove custom color names
coordset | show specific coordinate set (a.k.a. frame or conformer)
crossfade | fade from one view to another
defattr | set many Python attribute values for structure elements from a file
delete | delete parts of a structure
dssp | compute/assign secondary structure
exit | quit ChimeraX
quit | quit ChimeraX
fly | interpolate motions for animations
getcrd | report atomic coordinates
graphics | control 3D graphics parameters
hide | stop displaying (parts of) a model
~show | stop displaying (parts of) a model
~display | stop displaying (parts of) a model
lighting | change lighting
lighting model | change per-model lighting
material | change visual surface properties of 3D objects
measure buriedarea | measure surface area buried by contacting structures
measure center | measure center of mass of maps or atoms
measure convexity | color surface based on local convexity
measure correlation | measure correlation coefficient between two maps
measure inertia | measure moments of inertia
measure length | measure path length of connected markers
measure rotation | measure rotation of one model relative to another
measure symmetry | compute map symmetry
move | move (parts of) a model relative to others
move cofr | move models to center of rotation
palette | list available color palettes
perframe | execute commands every frame
~perframe | stop execution of commands every frame
pwd | report current working directory
rainbow | "rainbow" color (parts of) structures
rename | change name or ID of model
ribbon | show stylized representation of structure
~ribbon | stop show stylized representation of structure
rmsd | measure RMSD between two sets of atoms
rock | rock models back and forth
roll | continuously turn model(s) about an axis
runscript | run a Python script with arguments
select | select models or parts thereof
~select | unselect models or parts thereof
set | set various global parameters
~set | revert various global parameters to their default value
setattr | set Python attribute values for structure elements
show | display (parts of) a model
display | display (parts of) a model
size | change display size of structural elements
split | split a model into multiple models
stop | stop an ongoing motion
style | change style of depiction for strcutural elements
sym | generate symmetry mates
tile | tile models onto grid
~tile | untile models
time | time execution and redisplay of commands
transparency | change transparency of (parts of) models
turn | rotate a model about an axis
undo | undo a command
redo | redo an undone command
usage | show the required syntax for a command
version | report ChimeraX version number
view | change/save/restore 3D view
wait | wait a given amount of frames before executing the next command
windowsize | set the size of the 3D window
wobble | move models in figure 8 motion
worm | turn on/off worm depiction
~worm | turn off worm depiction
select zone | select (parts of) models within a 3D zone
zoom | zoom in/out
Selectors:
sel | selected atoms
all | everything
pbonds | pseudobonds
pbondatoms | pseudobond atoms
hbonds | hydrogen bonds
hbondatoms | hydrogen bond atoms
* STL (1.0.1): STL file read/write
Category: Generic 3D objects
This bundle provides the ability to read and write StereoLithography (STL)
files.
* Storm (1.0): STORM file reader
Category: Generic 3D object
Read STORM microscopy text files with x,y,z points and widths.
* StructMeasure (1.2.1): Structure measurement user interface
Category: Structure Analysis
Structure measurement tool, mouse mode, and context-menu entry
Tools:
---
Distances | inter-atomic distances
Angles/Torsions | report angle/torsion values
Axes/Planes/Centroids | create/analyze axes/planes/centroids
* Struts (1.0.1): struts for 3D printing
Category: Molecular structure
Add bonds between atoms of a molecule to strengthen it for 3-d printing.
Commands:
---
struts | provide struts for 3D printing
~struts | remove 3D printing struts
* Surface (1.0.1): Surface calculations
Category: Generic 3D objects
Routines to calculate and manipulate triangulated surfaces.
Tools:
---
Hide Dust | hide small surface blobs
Surface Zone | show surface near atoms
Color Zone | color surface to match nearby atoms
Measure Volume and Area | measure surface area and enclosed volume
Surface Color | Color surface by geometry or map value
Commands:
color electrostatic | color surface by electrostatic potential map
color sample | color surface by map value
color gradient | color surface by map gradient norm
color radial | color surface by distance from a point
color cylindrical | color surface by distance from an axis
color height | color surface by distance from a plane
color image | color surface using an image file
surface | create/modify surfaces
~surface | delete surface
surface showPatches | show atom surface patches for existing surfaces
surface hidePatches | hide patches of existing surfaces for specified atoms
surface close | close surfaces for specified atoms
surface style | set surface mesh, solid, or dot display style
surface squaremesh | mask mesh lines that are not parallel x, y or z
surface showall | turn of maskig of triangles and edges
surface cap | control surface caps when clipping
surface dust | hide small pieces of surfaces
surface undust | show small pieces of surfaces
surface invertShown | Show hidden part of surface and hide shown part
surface transform | Scale, rotate or move surfaces
surface zone | show surface near atoms
surface unzone | show all of surface
surface check | check surface topology
surface splitbycolor | Split surface by color
sop | alias for surface commands
volume splitbyzone | split volume by color zone
measure sasa | measure solvent-accessible surface area
measure volume | measure enclosed surface volume
measure area | measure surface area
measure contactArea | measure and contact area between two surfaces
* SwapAA (2.0.1): Swap amino acid
Category: Structure Editing
Swap amino acid
Command:
---
swapaa mousemode | Replaces amino acid with a specified standard amino acid
* SwapRes (2.5): Swap residue side chains
Category: Structure Editing
Swap amino/nucleic acid side chains, using rotamer libraries where applicable
Tool:
---
Rotamers | swap amino acid residue side chain
Commands:
swapaa | swap amino acid residue side chain
swapna | swap nucleic acid residue side chain
* TapeMeasure (1.0): Tape measure mouse mode
Category: General
Measure distance between two points in scene
* TaskManager (1.0): Manage background tasks in ChimeraX
Category: User Interface
Manage background tasks in ChimeraX
Tool:
---
Task Manager | Visualize open tasks
Command:
taskman | Visualize open tasks
* Test (1.0): simple regression test
Category: General
Execute a series of commands to test for regressions.
Commands:
---
debug test | Run through test sequence of commands to check for errors
debug exectest | Test running executable from bundle
debug expectfail | Expect command to fail
* Toolbar (1.1.2): Toolbar
Category: General
Tabbed Toolbar
Provides a Windows ribbon-style toolbar interface
Tool:
---
Toolbar | a Windows ribbon-style toolbar
* ToolshedUtils (1.2.4): Toolshed bundle utilities
Category: Utilities
Utilties for installing, uninstalling, and updating bundles from the ChimeraX
Toolshed
Tool:
---
Updates | install/update ChimeraX bundles from the Toolshed (web repository)
* Topography (1.0): Show a topographic surface for a 2D image
Category: Volume Data
Show a topographic surface for a 2D image.
Command:
---
topography | Show topographic surface
* ToQuest (1.0): Copy scenes to VR Quest headset
Category: General
Copy scene as GLTF for Quest Lookie VR app
Tool:
---
Send to Quest | Send scenes to Quest headset Lookie app
* Tug (1.0.1): Tug on atoms with molecular dynamics
Category: Molecular structure
Tug on atoms with molecular dynamics.
Command:
---
tug | No synopsis given
* UI (1.39.1): ChimeraX user interface
Category: User Interface
ChimeraX user interface
Commands:
---
ui | control user interface behavior
tool | Manipulate tools
* uniprot (2.3): UniProt database support
Category: Sequence
Fetch Uniprot sequence info
* UnitCell (1.0.1): Show crystal unit cell
Category: Higher-Order Structure
Copy an atomic model solved by X-ray crystallography to fill out the unit
cell.
Tool:
---
Unit Cell | Show crystal unit cell
Command:
unitcell | Place copies of atomic structure in crystal unit cell
* ViewDockX (1.4.3): Analyze ligand-receptor docking results
Category: General
Display docking results as structures and table.
UCSF DOCK output in PDB and mol2 formats are supported.
Tool:
---
ViewDockX | display docking results
Commands:
viewdockx | specify models as docking results
viewdockx down | Simulate down-arrow key in ViewDockX
viewdockx up | Simulate up-arrow key in ViewDockX
* VIPERdb (1.0): Read Virus Particle Explorer .vdb files
Category: Structure Analysis
Opens VIPERdb .vdb files and applies 60-fold icosahedral symmetry.
* Vive (1.1): Virtual reality headset support
Category: General
Use virtual reality headsets with SteamVR.
Commands:
---
vr | Render to virtual reality headsets using SteamVR
xr | Render to virtual reality headsets using OpenXR
device vr | Render to virtual reality headsets
* VolumeMenu (1.0.1): Volume menu
Category: Volume data
Add a top level volume menu.
Tool:
---
Show Volume Menu | Add a top level volume menu
* vrml (1.0): Write basic VRML output for 3D color printing
Category: Generic 3D objects
Write vertex colored VRML output for 3D color printing.
* VTK (1.0): Legacy VTK file reader and writer
Category: Generic 3D objects
The ChimeraX-VTK bundle provides support for reading
polygonal data from legacy VTK files and writing those files for molecular structures and surfaces.
* WavefrontOBJ (1.0): Wavefront OBJ file read/write
Category: Generic 3D objects
This bundle provides the ability to read and write Wavefront OBJ files.
* WebCam (1.0.2): Combine camera video with graphics
Category: General
Produce augmented reality videos combining web cam
video with rendered graphics.
Commands:
---
webcam | Show webcam video
device webcam | Show webcam video
* WebServices (1.1.4): Web service and HTTP request support
Category: General
Infrastructure support for web services and HTTP requests
* Zone (1.0.1): Mouse mode to show atom and map zones
Category: Volume Data
Display atoms and density near an atom chosen with the mouse
Command:
---
zone | Show atoms and map in a small region
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac
Model Identifier: Mac15,3
Model Number: Z1C80001JLL/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2 (23C64)
Kernel Version: Darwin 23.2.0
Time since boot: 105 days, 4 hours, 13 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (1)
comment:1 by , 16 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Tool Shed |
| Owner: | set to |
| Platform: | → all |
| Priority: | normal → high |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Toolshed can't find ArtiaX bundle |
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Reported by Josh Hutchings