Science Score: 54.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
23 of 34 committers (67.6%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.9%) to scientific vocabulary
Repository
Source code for molecular graphics program UCSF ChimeraX
Basic Info
- Host: GitHub
- Owner: RBVI
- License: other
- Language: Python
- Default Branch: develop
- Homepage: https://www.rbvi.ucsf.edu/chimerax/
- Size: 120 MB
Statistics
- Stars: 204
- Watchers: 8
- Forks: 36
- Open Issues: 58
- Releases: 3
Metadata Files
README.md
UCSF ChimeraX Molecular Visualization
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
- Repositories: 49
- Profile: https://github.com/RBVI
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:
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affiliation: "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA"
family-names: Pettersen
given-names: "Eric F."
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affiliation: "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA"
family-names: Goddard
given-names: "Thomas D."
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affiliation: "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA"
family-names: Huang
given-names: "Conrad C."
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affiliation: "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA"
family-names: Meng
given-names: "Elaine C."
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affiliation: "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA"
family-names: Couch
given-names: "Gregory S."
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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
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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
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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
Top Committers
| Name | 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... | ||
Committer Domains (Top 20 + Academic)
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
- actions/checkout v3 composite
- msys2/setup-msys2 v2 composite
- c-blosc *
- hdf5 *
- lz4 *
- netcdf *
- openblas *
- python@3.10 *