chimerax

Source code for molecular graphics program UCSF ChimeraX

https://github.com/rbvi/chimerax

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • CITATION.cff file
    Found CITATION.cff file
  • codemeta.json file
    Found codemeta.json file
  • .zenodo.json file
    Found .zenodo.json file
  • DOI references
  • Academic publication links
  • Committers with academic emails
    23 of 34 committers (67.6%) from academic institutions
  • Institutional organization owner
  • JOSS paper metadata
  • Scientific vocabulary similarity
    Low similarity (15.9%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

Source code for molecular graphics program UCSF ChimeraX

Basic Info
Statistics
  • Stars: 204
  • Watchers: 8
  • Forks: 36
  • Open Issues: 58
  • Releases: 3
Created over 5 years ago · Last pushed 7 months ago
Metadata Files
Readme License Citation Copyright

README.md

UCSF ChimeraX Molecular Visualization

Nightly Build Status Documentation Status User Documentation Twitter follow link

ChimeraX is an application for visualizing and analyzing molecule structures such as proteins, RNA, DNA, lipids as well as gene sequences, electron microscopy maps, X-ray maps, 3D light microscopy and 3D medical imaging scans. It is the successor of the UCSF Chimera program. Example images and feature highlights show a few of its capabilities, and recipes show example command and Python API use.

Installing ChimeraX

Nightly builds and semi-annual releases are available for Windows, macOS and Linux operating systems from the ChimeraX downloads page.

Platforms

ChimeraX runs on Windows, macOS and Linux and is free for academic and government use (license). Commercial use requires a fee which supports development of the software. It is about 80% Python 3 code and 20% C++ code. The C++ is for speed critical parts. It uses the Qt window toolkit.

Developing Plugins

The ChimeraX Programming Manual describes the Python APIs available.

ChimeraX plugins are called bundles and can include reading new file formats, adding commands, adding GUI interfaces for new analysis tools, new visualization methods for data, new mouse modes using Python and C++ languages. See the ChimeraX Developer Tutorial for information about creating bundles.

Building ChimeraX

Building ChimeraX can be challenging because it depends on more than 50 third party libraries and packages. We recommend using a prebuilt ChimeraX from the downloads page instead. If you develop your own ChimeraX plugins they can be used with a prebuilt ChimeraX using the toolshed install command.

Owner

  • Name: RBVI
  • Login: RBVI
  • Kind: organization

Citation (CITATION.cff)

# YAML 1.2
---
abstract: "UCSF ChimeraX is the next-generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX brings (a) significant performance and graphics enhancements; (b) new implementations of Chimera's most highly used tools, many with further improvements; (c) several entirely new analysis features; (d) support for new areas such as virtual reality, light-sheet microscopy, and medical imaging data; (e) major ease-of-use advances, including toolbars with icons to perform actions with a single click, basic \"undo\" capabilities, and more logical and consistent commands; and (f) an app store for researchers to contribute new tools. ChimeraX includes full user documentation and is free for noncommercial use, with downloads available for Windows, Linux, and macOS from https://www.rbvi.ucsf.edu/chimerax."
authors: 
  -
    affiliation: "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA"
    family-names: Pettersen
    given-names: "Eric F."
  -
    affiliation: "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA"
    family-names: Goddard
    given-names: "Thomas D."
  -
    affiliation: "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA"
    family-names: Huang
    given-names: "Conrad C."
  -
    affiliation: "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA"
    family-names: Meng
    given-names: "Elaine C."
  -
    affiliation: "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA"
    family-names: Couch
    given-names: "Gregory S."
  -
    affiliation: "Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge, UK"
    family-names: Croll
    given-names: "Tristan I."
    orcid: https://orcid.org/0000-0002-3514-8377
  -
    affiliation: "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA"
    family-names: Morris
    given-names: "John H."
    orcid: https://orcid.org/0000-0003-0290-7979
  -
    affiliation: "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA"
    family-names: Ferrin
    given-names: "Thomas E."
    orcid: https://orcid.org/0000-0001-6227-0637
cff-version: "1.1.0"
date-released: 2021-01-01
doi: "10.1002/pro.3943"
keywords: 
  - cryoEM
  - "density maps"
  - "interactive visualization and analysis"
  - "molecular graphics"
  - "molecular modeling"
  - "structural biology"
  - "virtual reality"
message: "If you use this software, please cite it using these metadata."
title: "UCSF ChimeraX: Structure visualization for researchers, educators, and developers"
version: "development"

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 19,694
  • Total Committers: 34
  • Avg Commits per committer: 579.235
  • Development Distribution Score (DDS): 0.691
Past Year
  • Commits: 1,514
  • Committers: 8
  • Avg Commits per committer: 189.25
  • Development Distribution Score (DDS): 0.682
Top Committers
Name Email Commits
Tom Goddard g****d@s****t 6,092
Eric Pettersen p****t@c****u 4,998
Greg Couch g****c@c****u 2,517
Conrad Huang c****d@c****u 1,310
Elaine Meng m****g@c****u 1,046
gregcouch g****h@g****m 694
Zach Pearson z****h@z****s 618
Zach Pearson z****p@c****u 486
Tom Goddard g****d@T****n 474
Elaine Meng e****g@g****m 346
Tom Goddard g****d@d****u 342
Tom Goddard g****d@c****u 330
Tom Goddard g****d@d****u 243
Tom Goddard g****d@T****n 90
Tom Goddard g****d@h****u 31
Tom Goddard g****d@T****l 25
Greg Couch g****c@c****u 11
Tom Goddard g****d@T****l 9
Scooter Morris s****r@c****u 8
Tom Goddard g****d@T****n 4
Tom Goddard g****d@T****l 3
Conrad Huang c****d@d****u 2
Tom Goddard g****d@h****u 2
Conrad Huang c****d@c****u 2
tferrin t****f@p****u 2
Tom Goddard g****d@h****u 1
Eric Pettersen p****t@k****u 1
Greg Couch g****h@g****m 1
Greg Couch g****c@b****u 1
Conrad Huang c****d@u****u 1
and 4 more...

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 13
  • Total pull requests: 138
  • Average time to close issues: 10 days
  • Average time to close pull requests: 9 days
  • Total issue authors: 11
  • Total pull request authors: 8
  • Average comments per issue: 1.69
  • Average comments per pull request: 0.3
  • Merged pull requests: 41
  • Bot issues: 0
  • Bot pull requests: 107
Past Year
  • Issues: 6
  • Pull requests: 137
  • Average time to close issues: 10 days
  • Average time to close pull requests: 9 days
  • Issue authors: 6
  • Pull request authors: 7
  • Average comments per issue: 1.83
  • Average comments per pull request: 0.31
  • Merged pull requests: 40
  • Bot issues: 0
  • Bot pull requests: 107
Top Authors
Issue Authors
  • RodenLuo (2)
  • alphataubio (2)
  • aretaon (1)
  • galeo (1)
  • pmaxwellward (1)
  • fses91 (1)
  • xiao1wen2 (1)
  • MatteoRiva95 (1)
  • s1752729916 (1)
  • dorkylever (1)
  • knight-hzj (1)
Pull Request Authors
  • dependabot[bot] (107)
  • pRottinghuis (20)
  • zjp (4)
  • alphataubio (2)
  • RodenLuo (2)
  • hfswetton (1)
  • benmwebb (1)
  • odcambc (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (107) python (106) github_actions (1)

Dependencies

.github/workflows/nightly.yml actions
  • actions/checkout v3 composite
  • msys2/setup-msys2 v2 composite
Brewfile homebrew
  • c-blosc *
  • hdf5 *
  • lz4 *
  • netcdf *
  • openblas *
  • python@3.10 *