Paper Published: MolViewSpec Toolkit

10/08 

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 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

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