Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Molecular Models02:00

Molecular Models

38.2K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
38.2K
UV–Vis Spectroscopy: Molecular Electronic Transitions01:16

UV–Vis Spectroscopy: Molecular Electronic Transitions

1.4K
In Ultraviolet–Visible (UV–Vis) spectroscopy, the absorption of electromagnetic radiation is used to probe the electronic structure of molecules. This technique provides insights into molecular electronic transitions, particularly the movement of electrons between different molecular orbitals. Radiation is absorbed if the energy of the electromagnetic radiation passing through the molecule is precisely equal to the energy difference between the excited and ground states. During this...
1.4K
Ultraviolet and Visible (UV–Vis) Spectroscopy: Overview01:02

Ultraviolet and Visible (UV–Vis) Spectroscopy: Overview

2.6K
Ultraviolet–visible (UV–visible or UV–Vis) spectroscopy is an analytical technique that investigates the interaction between matter and UV–Vis light within the electromagnetic spectrum. This method is widely used for its versatility, simplicity, and relatively quick data acquisition, making it valuable for both qualitative and quantitative analysis. When UV–Vis radiation passes through a material,  molecules absorb light depending on the energy required for...
2.6K
Molecular Shapes01:18

Molecular Shapes

56.8K
Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
Two regions of electron density in a diatomic...
56.8K
Imaging Biological Samples with Optical Microscopy01:18

Imaging Biological Samples with Optical Microscopy

4.7K
Optical microscopy uses optic principles to provide detailed images of samples. Antonie van Leeuwenhoek designed the first compound optical microscope in the 17th century to visualize blood cells, bacteria, and yeast cells. In 1830, Joseph Jackson Lister created an essentially modern light microscope. The 20th century saw the development of microscopes with enhanced magnification and resolution.
In optical microscopy, the specimen to be viewed is placed on a glass slide and clipped on the stage...
4.7K
Molecular Geometry and Dipole Moments02:36

Molecular Geometry and Dipole Moments

12.9K
The VSEPR theory can be used to determine the electron pair geometries and molecular structures as follows:
12.9K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Towards globally equitable bioinformatics adoption.

PLoS biology·2026
Same author

PDBe-SIFTS: an open-source tool for Structure Integration with Function, Taxonomy, and Sequences, featuring improved alignment, scoring scheme, and accelerated search.

bioRxiv : the preprint server for biology·2026
Same author

Generating 3D models of complex carbohydrates with GLYCAM-Web.

Nature methods·2026
Same author

MolViewStories: Interactive molecular storytelling.

Protein science : a publication of the Protein Society·2026
Same author

Mol* web molecular graphics engine.

Protein science : a publication of the Protein Society·2026
Same author

OSTM1 is a ubiquitin E3 ligase that suppresses B-cell malignancy by activating the cAMP/PKA/CREB pathway.

bioRxiv : the preprint server for biology·2026
Same journal

A Novel Laboratorial Approach to Evaluate Bacterial Microleakage of Endodontic Sealers.

Current protocols·2026
Same journal

TRIAGE Toolkit: Streamlined Discovery of Regulatory Genes and Elements.

Current protocols·2026
Same journal

High-throughput Profiling of Pseudouridines in Microbiome-derived Bacterial RNA.

Current protocols·2026
Same journal

Recombinant Protein Expression in Rhodococcus species.

Current protocols·2026
Same journal

Streamlined In Vitro Transcription for Generating Self-Amplifying RNA With Modified Nucleotides.

Current protocols·2026
Same journal

CODEC Library Preparation From Genomic DNA.

Current protocols·2026
See all related articles

Related Experiment Video

Updated: Jun 20, 2025

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

9.8K

Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit.

Sebastian Bittrich1, Adam Midlik2, Mihaly Varadi2

  • 1Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, California.

Current Protocols
|July 18, 2024
PubMed
Summary
This summary is machine-generated.

MolViewSpec simplifies macromolecular structure visualization by decoupling specifications from specific molecular viewers, enabling reproducible and interoperable 3D views for structural bioinformatics and life sciences education.

Keywords:
3D visualizationProtein Data Bankinteroperabilitymacromolecular structuremmCIF

More Related Videos

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
05:00

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

1.2K
Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

1.3K

Related Experiment Videos

Last Updated: Jun 20, 2025

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

9.8K
Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
05:00

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

1.2K
Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

1.3K

Area of Science:

  • Structural Bioinformatics
  • Computational Biology
  • Life Sciences Education

Background:

  • Molecular viewers offer accessible macromolecular structure visualization but face interoperability challenges due to technical intricacies and data integration complexities.
  • Reproducible data visualizations are crucial but hindered by the lack of standardized approaches across different molecular visualization tools.

Purpose of the Study:

  • Introduce MolViewSpec, a specification approach to define molecular visualizations independently of specific molecular viewer implementations.
  • Demonstrate the utility of MolViewSpec and its Python library for creating customized, sophisticated 3D molecular views.

Main Methods:

  • Developed MolViewSpec, a specification approach for defining molecular visualizations.
  • Created a 3D view-building Python library to implement MolViewSpec protocols.
  • Utilized MolViewSpec to support various representations (e.g., cartoon, ball-and-stick) with customization (coloring, labeling, transformations like superposition).

Main Results:

  • MolViewSpec successfully decouples visualization specifications from viewer implementations, enhancing interoperability.
  • The Python library enables the creation of customized 3D views for macromolecular structures in mmCIF, BinaryCIF, and PDB formats.
  • Demonstrated advanced features including labeling and complex transformations like superposition.

Conclusions:

  • MolViewSpec advances reusability and interoperability in molecular 3D visualization.
  • The specification approach addresses the timely need for handling large-scale molecular structures in structural bioinformatics and life sciences.
  • Facilitates reproducible and accessible molecular visualization for research and education.