The goal of Mol* (/'mol-star/) is to provide a technology stack that serves as a basis for the next-generation data delivery and analysis tools for (not only) macromolecular structure data. Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB) viewers.
When using Mol*, please cite:
David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures, Nucleic Acids Research, 2021; https://doi.org/10.1093/nar/gkab314.
The pdbe-molstar library is the Mol* implementation used by EMBL-EBI data resources such as PDBe, PDBe-KB and AlphaFold DB. This implementation can be used as a JS plugin and a Web component and supports property/attribute-based easy customisation. It provides helper methods to facilitate programmatic interactions between the web application and the 3D viewer. It also provides a superposition view for overlaying all the observed ligand molecules on representative protein conformations.
rcsb-molstar is the Mol* plugin used by RCSB PDB. The project provides additional presets for the visualization of structure alignments and structure motifs such as ligand binding sites. Furthermore, rcsb-molstar allows to interactively add or hide of (parts of) chains, as seen in the 3D Protein Feature View.
The core of Mol* consists of these modules (see under src/):
mol-task Computation abstraction with progress tracking and cancellation support.mol-data Collections (integer-based sets, interface to columns/tables, etc.)mol-math Math related (loosely) algorithms and data structures.mol-io Parsing library. Each format is parsed into an interface that corresponds to the data stored by it. Support for common coordinate, experimental/map, and annotation data formats.mol-model Data structures and algorithms (such as querying) for representing molecular data (including coordinate, experimental/map, and annotation data).mol-model-formats Data format parsers for mol-model.mol-model-props Common "custom properties".mol-script A scripting language for creating representations/scenes and querying (includes the MolQL query language).mol-geo Creating (molecular) geometries.mol-theme Theming for structure, volume and shape representations.mol-repr Molecular representations for structures, volumes and shapes.mol-gl A wrapper around WebGL.mol-canvas3d A low-level 3d view component. Uses mol-geo to generate geometries.mol-state State representation tree with state saving and automatic updates.mol-plugin Allow to define modular Mol* plugin instances utilizing mol-state and mol-canvas3d.mol-plugin-state State transformations, builders, and managers.mol-plugin-ui React-based user interface for the Mol* plugin. Some components of the UI are usable outside the main plugin and can be integrated into 3rd party solutions.mol-util Useful things that do not fit elsewhere.Moreover, the project contains the implementation of servers, including
servers/model A tool for accessing coordinate and annotation data of molecular structures.servers/volume A tool for accessing volumetric experimental data related to molecular structures.servers/plugin-state A basic server to store Mol* Plugin states.The project also contains performance tests (perf-tests), examples, and cli apps (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
This project builds on experience from previous solutions:
npm install
npm run build
npm run watch
If working on just the viewer, npm run watch-viewer will provide shorter compile times.
DEBUG=molstar npm run watch
Debug/production mode in browsers can be turned on/off during runtime by calling setMolStarDebugMode(true/false, true/false) from the dev console.
npm run clean
Wipes the build and lib directories and .tsbuildinfo files.
npm run rebuild
Runs the cleanup script prior to building the project, forcing a full rebuild of the project.
Use these commands to resolve occassional build failures which may arise after some dependency updates. Once done, npm run build should work again. Note that full rebuilds take more time to complete.
NODE_ENV=production npm run build
Run
If not installed previously:
npm install -g http-server
...or a similar solution.
From the root of the project:
http-server -p PORT-NUMBER
and navigate to build/viewer
CIF schemas
node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/mmcif.ts -p mmCIF
node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/ccd.ts -p CCD
node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/bird.ts -p BIRD
node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/cif-core.ts -p CifCore -aa
Lipid names
node lib/commonjs/cli/lipid-params -o src/mol-model/structure/model/types/lipids.ts
Ion names
node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-ions.js src/mol-model/structure/model/types/ions.ts
Saccharide names
node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-saccharides.js src/mol-model/structure/model/types/saccharides.ts
GraphQL schemas
node node_modules/@graphql-codegen/cli/cjs/bin -c src/extensions/rcsb/graphql/codegen.yml
Create chem comp bond table
node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-table.js build/data/ccb.bcif -b
Test model server
export NODE_PATH="lib"; node build/src/servers/model/test.js
State Transformer Docs
export NODE_PATH="lib"; node build/state-docs
Convert any CIF to BinaryCIF (or vice versa)
node lib/commonjs/servers/model/preprocess -i file.cif -ob file.bcif
To see all available commands, use node lib/commonjs/servers/model/preprocess -h.
Or
node lib/commonjs/cli/cif2bcif
E.g.
node lib/commonjs/cli/cif2bcif src.cif out.bcif.gz
node lib/commonjs/cli/cif2bcif src.bcif.gz out.cif
If node complains about a missing acorn peer dependency, run the following commands
npm update acorn --depth 20
npm dedupe
To get syntax highlighting for shader and graphql files add the following to Visual Code's settings files and make sure relevant extensions are installed in the editor.
"files.associations": {
"*.glsl.ts": "glsl",
"*.frag.ts": "glsl",
"*.vert.ts": "glsl",
"*.gql.ts": "graphql"
},
npm version prerelease # assumes the current version ends with '-dev.X'
npm publish --tag next
npm version 0.X.0 # provide valid semver string
npm publish
npm run test
npm run build
node ./scripts/deploy.js # currently updates the viewer on molstar.org/viewer
Just open an issue or make a pull request. All contributions are welcome.
Funding sources include but are not limited to:
[v3.35.0] - 2023-05-14
struct_conn records referencing watersPluginState.setSnapshot triggering unnecessary state updatesmol-state's State when trying to apply a transform to an existing Null objectSbNcbrPartialCharges extension for coloring and labeling atoms and residues by partial atomic charges
_sb_ncbr_partial_atomic_charges_meta and _sb_ncbr_partial_atomic_charges (more info in README.md)ignoreHydrogens in interactions representationlabel_asym_id if REMARK 350 is present)core.math in mol-script
cantorPairing, sortedCantorPairing, invertCantorPairing,trunc, signFAQs
A comprehensive macromolecular library.
The npm package molstar receives a total of 29,132 weekly downloads. As such, molstar popularity was classified as popular.
We found that molstar demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 0 open source maintainers collaborating on the project.
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