Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F24%3A00139730" target="_blank" >RIV/00216224:14310/24:00139730 - isvavai.cz</a>
Result on the web
<a href="https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.1099" target="_blank" >https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.1099</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1002/cpz1.1099" target="_blank" >10.1002/cpz1.1099</a>
Alternative languages
Result language
angličtina
Original language name
Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit
Original language description
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: , GitHub project: ), 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. (c) 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: Creating a MolViewSpec view using the MolViewSpec Python packageBasic Protocol 2: Creating a MolViewSpec view with reference to MolViewSpec annotation filesBasic Protocol 3: Creating a MolViewSpec view with labels and other advanced featuresSupport Protocol 1: Computing rotation and translation vectorsSupport Protocol 2: Creating a MolViewSpec annotation file
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Result continuities
Project
<a href="/en/project/GM22-30571M" target="_blank" >GM22-30571M: Cell*: a web platform for visualization, modelling and dynamics of organnel- and cell-sized structures</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2024
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Current Protocols
ISSN
2691-1299
e-ISSN
2691-1299
Volume of the periodical
4
Issue of the periodical within the volume
7
Country of publishing house
US - UNITED STATES
Number of pages
23
Pages from-to
1-23
UT code for WoS article
001270762400001
EID of the result in the Scopus database
2-s2.0-85198756612