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Developers: Switch to Sequence Coordinates Service by May 31, 2025
The new Sequence Coordinates Service supports better access to RCSB PDB features
A new Sequence Coordinates Service more effectively integrates the growing number of protein structures and introduces several minor API changes to better support access to RCSB PDB features.
The old 1D Coordinates Service API will remain operational for a limited period ending May 31, 2025.
Please contact RCSB PDB with any questions or concerns.
Paper Published: MolViewSpec Toolkit
Figure 5: Result of Basic Protocol 2 described in Current Protocols (2024) 4: e1099 doi: 10.1002/cpz1.1099
MolViewSpec (GitHub) provides a generic mechanism for describing visual scenes or views that are used in molecular visualizations. It adopts a declarative data-driven approach to describe, load, render, and visually deliver molecular structures, along with 3D representations, coloring schemes, and associated structural, biological, or functional annotations. The toolkit allows for describing the information required for representing a molecular view state as data in a nested tree format that can be consumed by visualization software tools such as Mol*.provides a generic mechanism for describing visual scenes or views that are used in molecular visualizations. It adopts declarative data-driven approach to describe, load, render, and visually deliver molecular structures, along with 3D representations, coloring schemes, and associated structural, biological, or functional annotations. The toolkit allows for describing the information required for representing a molecular view state as data in a nested tree format that can be consumed by visualization software tools such as Mol*.
Protocols described in a new Current Protocols article demonstrate the application of MolViewSpec coupled with its Python-based 3D view–building library to craft intricate and tailored 3D visualizations.
- Basic Protocol 1: Creating a MolViewSpec view using the MolViewSpec Python package
- Basic Protocol 2: Creating a MolViewSpec view with reference to MolViewSpec annotation files
- Basic Protocol 3: Creating a MolViewSpec view with labels and other advanced features
- Support Protocol 1: Computing rotation and translation vectors
- Support Protocol 2: Creating a MolViewSpec annotation file
Describing and sharing molecular visualizations using the MolViewSpec toolkit.
S. Bittrich, A. Midlik, M. Varadi, S. Velankar, S.K. Burley, J.Y. Young, D. Sehnal, B. Vallat
(2024) Current Protocols 4: e1099 doi: 10.1002/cpz1.1099