Software Embedded in UCSF ChimeraX
UCSF ChimeraX is built upon other great software.
This information was generated from ChimeraX 1.11.dev202511050308 for Linux on 2025-11-05 03:08:38 UTC.
- Python version
3.11.13
- “The Python programming language and interpreter.”
History and License: open source
ChimeraX is distributed as Python packages,
either written in the Python language
or as a binary package written in C or C++.
- Rotamer libraries (amino acid sidechain conformations and associated information) from the following sources:
-
- FFmpeg version 3.2.4
- “A complete, cross-platform solution to record, convert and stream audio and video.”
License: GNU General Public License v3
Embedded licenses: FFmpeg embedded licences
FFmpeg is bundled as a convenience for users of ChimeraX.
It is a separate product,
and thus, its license does not affect ChimeraX's license.
FFmpeg can be freely redistributed separately from ChimeraX.
See the GPL FAQ for more details.
It can be found in the bin directory.
- Minicons Free Vector Icons Pack (downloaded 28 November 2016)
- The Minicons Free Vector Icon Pack is a free set of scalable icons.
License type: Creative Commons Abbtributions 3.0 Unported
Linux only.
- BasicProperty (and BasicTypes) for Python (downloaded 15 February 2018)
- The flatten function in basictypes/latebind.py is the basis for our chimerax.core.utils.flattened function. The Python packages are not included.
License type: BSD license
- cpp-peglib (downloaded 9 July 2024)
- The cpp-peglib library was written by Yuji Hirose and is used in ChimeraX to parse command-line specifiers.
License type: MIT license
- AmberTools
- Certain executables from the AmberTools package are included with ChimeraX in order to compute partial charges. These executables are unmodified relative to their AmberTools versions, and are communicated with via their normal inputs and outputs.
License: Most of AmberTools is covered under the GNU Public License v3.
For convenience,
the ChimeraX distribution includes the Python packages that it depends on.
Both the direct and indirect dependencies are shown below.
The package names are links to the home page of the corresponding Python package.
The license type is shown, and if a license is bundled with the package,
a link to it is provided.
Note: this list is automatically generated.
Packages:
aiohappyeyeballs, aiohttp, aiosignal, alabaster, annotated-types, anyio, appdirs, asttokens, attrs, babel, beautifulsoup4, blockdiag, blosc2, build, certifi, cftime, charset-normalizer, click, colorama, comm, contourpy, coverage, cxservices, cycler, Cython, debugpy, decorator, distro, docutils, executing, filelock, fonttools, frozenlist, funcparserlib, glfw, grako, h11, h5py, html2text, httpcore, httpx, httpx-sse, idna, ihm, imagecodecs, imagesize, iniconfig, ipykernel, ipython, ipython_pygments_lexers, ipywidgets, jedi, Jinja2, jsonschema, jsonschema-specifications, jupyter_client, jupyter_core, jupyterlab_widgets, kiwisolver, line_profiler, lxml, lz4, Markdown, MarkupSafe, matplotlib, matplotlib-inline, mcp, msgpack, multidict, ndindex, nest-asyncio, netCDF4, networkx, nibabel, nptyping, numexpr, numpy, nvidia-nvjitlink-cu12, OpenMM, OpenMM-CUDA-12, openvr, packaging, ParmEd, parso, pep517, pexpect, pickleshare, pillow, pip, pkginfo, platformdirs, pluggy, prompt_toolkit, propcache, psutil, ptyprocess, pure_eval, py-cpuinfo, pybind11, pycollada, pydantic, pydantic-settings, pydantic_core, pydicom, Pygments, pynmrstar, pynrrd, PyOpenGL, PyOpenGL-accelerate, pyopenxr, pyparsing, pyproject_hooks, PyQt6-commercial, PyQt6-Qt6, PyQt6-WebEngine-commercial, PyQt6-WebEngine-Qt6, PyQt6_sip, pytest, pytest-cov, python-dateutil, python-dotenv, python-multipart, pytz, pyzmq, qtconsole, QtPy, qtshim, RandomWords, referencing, requests, roman-numerals-py, rpds-py, scipy, setuptools, sfftk-rw, six, sniffio, snowballstemmer, sortedcontainers, soupsieve, Sphinx, sphinx-autodoc-typehints, sphinxcontrib-applehelp, sphinxcontrib-blockdiag, sphinxcontrib-devhelp, sphinxcontrib-htmlhelp, sphinxcontrib-jsmath, sphinxcontrib-qthelp, sphinxcontrib-serializinghtml, sse-starlette, stack-data, starlette, superqt, tables, tcia_utils, tifffile, tinyarray, tornado, traitlets, typing-inspection, typing_extensions, tzdata, urllib3, uvicorn, wcwidth, webcolors, wheel, wheel-filename, widgetsnbextension, yarl.
- aiohappyeyeballs version 2.6.1
- Happy Eyeballs for asyncio
License type: Python Software Foundation License
- aiohttp version 3.13.1
- Async http client/server framework (asyncio)
License type: Apache-2.0 AND MIT
- aiosignal version 1.4.0
- aiosignal: a list of registered asynchronous callbacks
License type: Apache Software License
- alabaster version 1.0.0
- A light, configurable Sphinx theme
License type: BSD License
- annotated-types version 0.7.0
- Reusable constraint types to use with typing.Annotated
License type: MIT License
- anyio version 4.11.0
- High-level concurrency and networking framework on top of asyncio or Trio
- appdirs version 1.4.4
- A small Python module for determining appropriate platform-specific dirs, e.g. a "user data dir".
License type: MIT License
- asttokens version 3.0.0
- Annotate AST trees with source code positions
License type: Apache 2.0
- attrs version 25.4.0
- Classes Without Boilerplate
- babel version 2.17.0
- Internationalization utilities
License type: BSD License
- beautifulsoup4 version 4.13.5
- Screen-scraping library
License type: MIT License
- blockdiag version 3.0.0
- blockdiag generates block-diagram image from text
License type: Apache Software License
- blosc2 version 3.11.0
- A fast & compressed ndarray library with a flexible compute engine.
License type: BSD License
- build version 1.3.0
- A simple, correct Python build frontend
- certifi version 2025.10.5
- Python package for providing Mozilla's CA Bundle.
License type: Mozilla Public License 2.0 (MPL 2.0)
- cftime version 1.6.5
- Time-handling functionality from netcdf4-python
- charset-normalizer version 3.4.4
- The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet.
License type: MIT
- click version 8.3.0
- Composable command line interface toolkit
- colorama version 0.4.6
- Cross-platform colored terminal text.
License type: BSD License
- comm version 0.2.3
- Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc.
License type: BSD License
- contourpy version 1.3.3
- Python library for calculating contours of 2D quadrilateral grids
License type: BSD License
- coverage version 7.11.0
- Code coverage measurement for Python
License type: Apache-2.0
- cxservices version 1.2.3
- RBVI ChimeraX Web Services
- cycler version 0.12.1
- Composable style cycles
License type: BSD License
- Cython version 3.1.4
- The Cython compiler for writing C extensions in the Python language.
License type: Apache Software License
- debugpy version 1.8.17
- An implementation of the Debug Adapter Protocol for Python
License type: MIT License
- decorator version 5.2.1
- Decorators for Humans
License type: BSD License
- distro version 1.9.0
- Distro - an OS platform information API
License type: Apache Software License
- docutils version 0.21.2
- Docutils -- Python Documentation Utilities
License type: Public Domain, Python Software Foundation License, BSD License, GNU General Public License (GPL)
- executing version 2.2.1
- Get the currently executing AST node of a frame, and other information
License type: MIT License
- filelock version 3.19.1
- A platform independent file lock.
License type: The Unlicense (Unlicense)
- fonttools version 4.60.1
- Tools to manipulate font files
License type: MIT
- frozenlist version 1.8.0
- A list-like structure which implements collections.abc.MutableSequence
License type: Apache-2.0
- funcparserlib version 2.0.0a0
- Recursive descent parsing library based on functional combinators
License type: MIT License
- glfw version 2.10.0
- A ctypes-based wrapper for GLFW3.
License type: MIT License
- grako version 3.16.5
- Grako (for "grammar compiler") takes a grammar in a variation of EBNF as input, and outputs a memoizing PEG/Packrat parser in Python.
License type: BSD License
- h11 version 0.16.0
- A pure-Python, bring-your-own-I/O implementation of HTTP/1.1
License type: MIT License
- h5py version 3.15.1
- Read and write HDF5 files from Python
- html2text version 2025.4.15
- Turn HTML into equivalent Markdown-structured text.
- httpcore version 1.0.9
- A minimal low-level HTTP client.
License type: BSD License
- httpx version 0.28.1
- The next generation HTTP client.
License type: BSD License
- httpx-sse version 0.4.3
- Consume Server-Sent Event (SSE) messages with HTTPX.
License type: MIT
- idna version 3.11
- Internationalized Domain Names in Applications (IDNA)
- ihm version 2.2
- Package for handling IHM mmCIF and BinaryCIF files
License type: MIT License
- imagecodecs version 2024.6.1
- Image transformation, compression, and decompression codecs
License type: BSD License
- imagesize version 1.4.1
- Getting image size from png/jpeg/jpeg2000/gif file
License type: MIT License
- iniconfig version 2.3.0
- brain-dead simple config-ini parsing
- ipykernel version 6.30.1
- IPython Kernel for Jupyter
License type: BSD 3-Clause License
Copyright (c) 2015, IPython Development Team
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- ipython version 9.5.0
- IPython: Productive Interactive Computing
License type: BSD License
- ipython_pygments_lexers version 1.1.1
- Defines a variety of Pygments lexers for highlighting IPython code.
License type: BSD License
- ipywidgets version 8.1.8
- Jupyter interactive widgets
License type: BSD License
- jedi version 0.19.2
- An autocompletion tool for Python that can be used for text editors.
License type: MIT License
- Jinja2 version 3.1.6
- A very fast and expressive template engine.
License type: BSD License
- jsonschema version 4.25.1
- An implementation of JSON Schema validation for Python
- jsonschema-specifications version 2025.9.1
- The JSON Schema meta-schemas and vocabularies, exposed as a Registry
- jupyter_client version 8.6.3
- Jupyter protocol implementation and client libraries
License type: BSD License
- jupyter_core version 5.9.1
- Jupyter core package. A base package on which Jupyter projects rely.
- jupyterlab_widgets version 3.0.16
- Jupyter interactive widgets for JupyterLab
License type: BSD License
- kiwisolver version 1.4.9
- A fast implementation of the Cassowary constraint solver
License type: BSD License
- line_profiler version 5.0.0
- Line-by-line profiler
License type: BSD License
- lxml version 6.0.2
- Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API.
License type: BSD-3-Clause
- lz4 version 4.3.2
- LZ4 Bindings for Python
License type: BSD License
- Markdown version 3.8.2
- Python implementation of John Gruber's Markdown.
- MarkupSafe version 3.0.3
- Safely add untrusted strings to HTML/XML markup.
- matplotlib version 3.10.7
- Python plotting package
License type: Python Software Foundation License
- matplotlib-inline version 0.2.1
- Inline Matplotlib backend for Jupyter
- mcp version 1.18.0
- Model Context Protocol SDK
License type: MIT License
- msgpack version 1.1.1
- MessagePack serializer
License type: Apache 2.0
- multidict version 6.7.0
- multidict implementation
License type: Apache License 2.0
- ndindex version 1.10.0
- A Python library for manipulating indices of ndarrays.
License type: MIT
- nest-asyncio version 1.6.0
- Patch asyncio to allow nested event loops
License type: BSD License
- netCDF4 version 1.6.5
- Provides an object-oriented python interface to the netCDF version 4 library
License type: MIT License
- networkx version 3.3
- Python package for creating and manipulating graphs and networks
License type: BSD License
- nibabel version 5.2.0
- Access a multitude of neuroimaging data formats
License type: MIT License
- nptyping version 2.5.0
- Type hints for NumPy.
License type: MIT License
- numexpr version 2.14.1
- Fast numerical expression evaluator for NumPy
- numpy version 1.26.4
- Fundamental package for array computing in Python
License type: BSD License
- nvidia-nvjitlink-cu12 version 12.9.86
- Nvidia JIT LTO Library
License type: Other/Proprietary License
- OpenMM version 8.2.0
- Python wrapper for OpenMM (a C++ MD package)
License type: Python Software Foundation License (BSD-like)
- OpenMM-CUDA-12 version 8.2.0
- CUDA platform for OpenMM
- openvr version 1.26.701
- Unofficial python bindings for Valve OpenVR SDK
License type: BSD License
- packaging version 25.0
- Core utilities for Python packages
License type: Apache Software License, BSD License
- ParmEd version 4.2.2
- Inter-package toolkit for molecular mechanical simulations
License type: LGPL
- parso version 0.8.5
- A Python Parser
License type: MIT License
- pep517 version 0.13.1
- Wrappers to build Python packages using PEP 517 hooks
License type: MIT License
- pexpect version 4.9.0
- Pexpect allows easy control of interactive console applications.
License type: ISC License (ISCL)
- pickleshare version 0.7.5
- Tiny 'shelve'-like database with concurrency support
License type: MIT License
- pillow version 11.3.0
- Python Imaging Library (Fork)
- pip version 25.2
- The PyPA recommended tool for installing Python packages.
- pkginfo version 1.12.1.2
- Query metadata from sdists / bdists / installed packages.
License type: MIT License
- platformdirs version 4.5.0
- A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`.
License type: MIT License
- pluggy version 1.6.0
- plugin and hook calling mechanisms for python
License type: MIT License
- prompt_toolkit version 3.0.52
- Library for building powerful interactive command lines in Python
License type: BSD License
- propcache version 0.4.1
- Accelerated property cache
License type: Apache Software License
- psutil version 7.0.0
- Cross-platform lib for process and system monitoring in Python. NOTE: the syntax of this script MUST be kept compatible with Python 2.7.
License type: BSD License
- ptyprocess version 0.7.0
- Run a subprocess in a pseudo terminal
License type: ISC License (ISCL)
- pure_eval version 0.2.3
- Safely evaluate AST nodes without side effects
License type: MIT License
- py-cpuinfo version 9.0.0
- Get CPU info with pure Python
License type: MIT License
- pybind11 version 3.0.1
- Seamless operability between C++11 and Python
- pycollada version 0.8
- python library for reading and writing collada documents
License type: BSD
- pydantic version 2.12.3
- Data validation using Python type hints
- pydantic-settings version 2.11.0
- Settings management using Pydantic
License type: MIT License
- pydantic_core version 2.41.4
- Core functionality for Pydantic validation and serialization
- pydicom version 2.4.4
- A pure Python package for reading and writing DICOM data
License type: MIT License
- Pygments version 2.18.0
- Pygments is a syntax highlighting package written in Python.
License type: BSD License
- pynmrstar version 3.3.6
- PyNMR-STAR provides tools for reading, writing, modifying, and interacting with NMR-STAR files. Maintained by the BMRB.
License type: MIT License
- pynrrd version 1.0.0
- Pure python module for reading and writing NRRD files.
License type: MIT License
- PyOpenGL version 3.1.10
- Standard OpenGL bindings for Python
License type: BSD License
- PyOpenGL-accelerate version 3.1.10
- Cython-coded accelerators for PyOpenGL
License type: BSD License
- pyopenxr version 1.1.4501
- Unofficial python bindings for OpenXR VR/AP device access
License type: Apache Software License
- pyparsing version 3.2.5
- pyparsing - Classes and methods to define and execute parsing grammars
- pyproject_hooks version 1.2.0
- Wrappers to call pyproject.toml-based build backend hooks.
License type: MIT License
- PyQt6-commercial version 6.9.1
- Python bindings for the Qt cross platform application toolkit
- PyQt6-Qt6 version 6.9.2
- The subset of a Qt installation needed by PyQt6.
License type: LGPL v3
- PyQt6-WebEngine-commercial version 6.9.0
- Python bindings for the Qt WebEngine framework
License type: Riverbank Commercial License
- PyQt6-WebEngine-Qt6 version 6.9.2
- The subset of a Qt installation needed by PyQt6-WebEngine.
License type: LGPL v3
- PyQt6_sip version 13.10.2
- The sip module support for PyQt6
License type: BSD-2-Clause
- pytest version 8.4.2
- pytest: simple powerful testing with Python
License type: MIT License
- pytest-cov version 7.0.0
- Pytest plugin for measuring coverage.
License type: MIT License
- python-dateutil version 2.9.0.post0
- Extensions to the standard Python datetime module
License type: BSD License, Apache Software License
- python-dotenv version 1.2.1
- Read key-value pairs from a .env file and set them as environment variables
- python-multipart version 0.0.20
- A streaming multipart parser for Python
License type: Apache Software License
- pytz version 2025.2
- World timezone definitions, modern and historical
License type: MIT License
- pyzmq version 27.1.0
- Python bindings for 0MQ
License type: BSD License
- qtconsole version 5.7.0
- Jupyter Qt console
License type: BSD License
- QtPy version 2.4.3
- Provides an abstraction layer on top of the various Qt bindings (PyQt5/6 and PySide2/6).
License type: MIT License
- qtshim version 1.2
- Qt shim that handles PyQt5/6 and PySide2/6
License type: Free for non-commercial use
- RandomWords version 0.4.0
- A useful module for a random text, e-mails and lorem ipsum.
License type: MIT License
- referencing version 0.37.0
- JSON Referencing + Python
- requests version 2.32.5
- Python HTTP for Humans.
License type: Apache Software License
- roman-numerals-py version 3.1.0
- Manipulate well-formed Roman numerals
License type: Zero-Clause BSD (0BSD), CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
- rpds-py version 0.28.0
- Python bindings to Rust's persistent data structures (rpds)
- scipy version 1.14.0
- Fundamental algorithms for scientific computing in Python
License type: BSD License
- setuptools version 80.9.0
- Easily download, build, install, upgrade, and uninstall Python packages
- sfftk-rw version 0.8.1
- Toolkit for reading and writing EMDB-SFF files
License type: Apache Software License
- six version 1.17.0
- Python 2 and 3 compatibility utilities
License type: MIT License
- sniffio version 1.3.1
- Sniff out which async library your code is running under
License type: MIT License, Apache Software License
- snowballstemmer version 3.0.1
- This package provides 32 stemmers for 30 languages generated from Snowball algorithms.
License type: BSD License
- sortedcontainers version 2.4.0
- Sorted Containers -- Sorted List, Sorted Dict, Sorted Set
License type: Apache Software License
- soupsieve version 2.8
- A modern CSS selector implementation for Beautiful Soup.
License type: MIT License
- Sphinx version 8.2.3
- Python documentation generator
- sphinx-autodoc-typehints version 3.2.0
- Type hints (PEP 484) support for the Sphinx autodoc extension
License type: MIT License
- sphinxcontrib-applehelp version 2.0.0
- sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books
License type: BSD License
- sphinxcontrib-blockdiag version 3.0.0
- Sphinx "blockdiag" extension
License type: BSD License
- sphinxcontrib-devhelp version 2.0.0
- sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents
License type: BSD License
- sphinxcontrib-htmlhelp version 2.1.0
- sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files
License type: BSD License
- sphinxcontrib-jsmath version 1.0.1
- A sphinx extension which renders display math in HTML via JavaScript
License type: BSD License
- sphinxcontrib-qthelp version 2.0.0
- sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents
License type: BSD License
- sphinxcontrib-serializinghtml version 2.0.0
- sphinxcontrib-serializinghtml is a sphinx extension which outputs "serialized" HTML files (json and pickle)
License type: BSD License
- sse-starlette version 3.0.3
- SSE plugin for Starlette
- stack-data version 0.6.3
- Extract data from python stack frames and tracebacks for informative displays
License type: MIT License
- starlette version 0.50.0
- The little ASGI library that shines.
- superqt version 0.7.6
- Missing widgets and components for PyQt/PySide
License type: BSD License
- tables version 3.10.2
- Hierarchical datasets for Python
License type: BSD License
- tcia_utils version 1.5.1
- A package to simplify common tasks one might perform when interacting with The Cancer Imaging Archive (TCIA) via Jupyter/Python.
License type: Apache Software License
- tifffile version 2025.3.13
- Read and write TIFF files
License type: BSD License
- tinyarray version 1.2.5
- Arrays of numbers for Python, optimized for small sizes
License type: BSD License
- tornado version 6.5.2
- Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed.
License type: Apache Software License
- traitlets version 5.14.3
- Traitlets Python configuration system
License type: BSD License
- typing-inspection version 0.4.2
- Runtime typing introspection tools
- typing_extensions version 4.15.0
- Backported and Experimental Type Hints for Python 3.9+
- tzdata version 2025.2
- Provider of IANA time zone data
License type: Apache Software License
- urllib3 version 2.5.0
- HTTP library with thread-safe connection pooling, file post, and more.
- uvicorn version 0.38.0
- The lightning-fast ASGI server.
- wcwidth version 0.2.14
- Measures the displayed width of unicode strings in a terminal
License type: MIT License
- webcolors version 24.11.1
- A library for working with the color formats defined by HTML and CSS.
License type: BSD License
- wheel version 0.45.1
- A built-package format for Python
License type: MIT License
- wheel-filename version 1.4.2
- Parse wheel filenames
License type: MIT License
- widgetsnbextension version 4.0.15
- Jupyter interactive widgets for Jupyter Notebook
License type: BSD License
- yarl version 1.22.0
- Yet another URL library
License type: Apache Software License