Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit Article Swipe
Sebastian Bittrich
,
Adam Midlik
,
Mihály Váradi
,
Sameer Velankar
,
S.K. Burley
,
Jasmine Young
,
David Sehnal
,
Brinda Vallat
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1002/cpz1.1099
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1002/cpz1.1099
With the ever‐expanding toolkit of molecular viewers, the ability to visualize macromolecular structures has never been more accessible. Yet, the idiosyncratic technical intricacies across tools and the integration complexities associated with handling structure annotation data present significant barriers to seamless interoperability and steep learning curves for many users. The necessity for reproducible data visualizations is at the forefront of the current challenges. Recently, we introduced MolViewSpec (homepage: https://molstar.org/mol‐view‐spec/ , GitHub project: https://github.com/molstar/mol‐view‐spec ), a specification approach that defines molecular visualizations, decoupling them from the varying implementation details of different molecular viewers. Through the protocols presented herein, we demonstrate how to use MolViewSpec and its 3D view–building Python library for creating sophisticated, customized 3D views covering all standard molecular visualizations. MolViewSpec supports representations like cartoon and ball‐and‐stick with coloring, labeling, and applying complex transformations such as superposition to any macromolecular structure file in mmCIF, BinaryCIF, and PDB formats. These examples showcase progress towards reusability and interoperability of molecular 3D visualization in an era when handling molecular structures at scale is a timely and pressing matter in structural bioinformatics as well as research and education across the life sciences. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. 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
Related Topics
Concepts
Computer science
Interoperability
Python (programming language)
Visualization
World Wide Web
Annotation
Protocol (science)
Toolbox
File format
Structural bioinformatics
Software engineering
Programming language
Artificial intelligence
Pathology
Physics
Medicine
Alternative medicine
Nuclear magnetic resonance
Protein structure
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1002/cpz1.1099
- OA Status
- hybrid
- Cited By
- 5
- References
- 24
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4400773957
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4400773957Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1002/cpz1.1099Digital Object Identifier
- Title
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Describing and Sharing Molecular Visualizations Using the MolViewSpec ToolkitWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2024Year of publication
- Publication date
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2024-07-01Full publication date if available
- Authors
-
Sebastian Bittrich, Adam Midlik, Mihály Váradi, Sameer Velankar, S.K. Burley, Jasmine Young, David Sehnal, Brinda VallatList of authors in order
- Landing page
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https://doi.org/10.1002/cpz1.1099Publisher landing page
- Open access
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YesWhether a free full text is available
- OA status
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hybridOpen access status per OpenAlex
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https://doi.org/10.1002/cpz1.1099Direct OA link when available
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Computer science, Interoperability, Python (programming language), Visualization, World Wide Web, Annotation, Protocol (science), Toolbox, File format, Structural bioinformatics, Software engineering, Programming language, Artificial intelligence, Pathology, Physics, Medicine, Alternative medicine, Nuclear magnetic resonance, Protein structureTop concepts (fields/topics) attached by OpenAlex
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5Total citation count in OpenAlex
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2025: 3, 2024: 2Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.superposition | 136 |
| abstract_inverted_index.visualization | 159 |
| abstract_inverted_index.bioinformatics | 177 |
| abstract_inverted_index.implementation | 86 |
| abstract_inverted_index.macromolecular | 12, 139 |
| abstract_inverted_index.sophisticated, | 111 |
| abstract_inverted_index.visualizations | 54 |
| abstract_inverted_index.representations | 122 |
| abstract_inverted_index.transformations | 133 |
| abstract_inverted_index.view–building | 106 |
| abstract_inverted_index.visualizations, | 80 |
| abstract_inverted_index.visualizations. | 119 |
| abstract_inverted_index.ever‐expanding | 3 |
| abstract_inverted_index.interoperability | 41, 155 |
| abstract_inverted_index.ball‐and‐stick | 126 |
| abstract_inverted_index.https://molstar.org/mol‐view‐spec/ | 68 |
| abstract_inverted_index.https://github.com/molstar/mol‐view‐spec | 72 |
| cited_by_percentile_year.max | 97 |
| cited_by_percentile_year.min | 94 |
| corresponding_author_ids | https://openalex.org/A5042417574, https://openalex.org/A5058986691 |
| countries_distinct_count | 3 |
| institutions_distinct_count | 8 |
| corresponding_institution_ids | https://openalex.org/I102322142, https://openalex.org/I1303153112, https://openalex.org/I21449261 |
| citation_normalized_percentile.value | 0.83129036 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |