AtomWorks Studio
Inspect, annotate and edit molecular structures in a browser, VS Code or PyMOL.
Documentation · Installation · Tutorial
Studio is a structure and annotation editor for AtomWorks annotated CIF files. Select atoms, attach conditioning annotations (sequence, coordinates, hotspots, index groups and more), fix bonds and charges, protonate, edit chains and expandable segments, and save a CIF that any Studio interface reopens. It is built for preparing inputs to structure-design models such as RFD4-Proteina. No model runtime or weights are needed.
Features
- One editor, three interfaces. The browser, VS Code and native PyMOL share annotation definitions, editing operations, CIF storage and Undo.
- Annotations you can see. Pick a condition, apply it to a selection, and color or inspect the stored values.
- Selections with AtomWorks queries. Expressions such as
chain_id == 'A' & res_id > 50work everywhere. - Structure edits with Undo. Bonds, charges, pH-based protonation, chains, segments and validation.
- Two renderers in the browser. Mol* (WebGL) by default and Patinae (WebGPU), both bundled.
- Design-ready examples. Protein and small-molecule binders, antibody and nanobody CDRs, enzyme motifs, motif scaffolding, inverse folding and partial diffusion.
- Optional Gradio host. Adds generation controls around the same editor for hosted demos and Spaces.
Install
Studio needs Python 3.12.
python -m pip install atomworks-studio
atomworks-studio
Open http://127.0.0.1:8000/. The guide is at http://127.0.0.1:8000/guide/. Mol* and Patinae are included in the package; Node and Rust are only needed to build from source.
| Browser and VS Code Run atomworks-studio, or install the VSIX from the
releases and run
AtomWorks: Open Studio. The extension starts its Python backend for you. |
PyMOL Install the package in PyMOL's Python environment, run atomworks-studio-pymol install, then open Plugin → AtomWorks Studio.
PyMOL and Qt come from your PyMOL installation. |
Use
Open a CIF, select atoms, and choose an annotation in Edit → Annotations. Inspect the stored values, change bonds or charges, protonate, or edit chains and segments. Save CIF writes a file that opens in any interface.
The PyMOL plugin offers the same controls natively, here on a nanobody design with a hotspot on the target:
See the documentation for selection syntax, interface guides, Python and HTTP integration, and development notes.
Build from source
make bootstrap
make test
make build
make run
The RFD4 annotation definitions and license are bundled in source and release builds and verified against the
SHA-256 hashes in providers/rfd4/UPSTREAM.toml. See provenance.
License
BSD-3-Clause. See LICENSE.md.
1 maintainer
Metadata
1 maintainer
Release files for atomworks-studio 0.0.2
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