Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Molecular Models

Molecular Models

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.

You might also read

Related Articles

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

Sort by

Same author

Author Correction: De novo design of quasisymmetric two-component protein cages.

Nature·2026

Same author

De novo design of quasisymmetric two-component protein cages.

Nature·2026

Same author

MX2 Mediates Collapse of the HIV-1 Capsid.

bioRxiv : the preprint server for biology·2026

Same author

A novel fusion tool to enable G protein-coupled receptor structure determination.

Acta crystallographica. Section D, Structural biology·2026

Same author

Using experimental results of protein design to guide biomolecular energy-function development.

PLoS computational biology·2026

Same author

Molecular insights into the capsular polysaccharide transporter Wza-Wzc complex.

Nature communications·2026

Same journal

iMUT-seq mapping of DSB-induced mutations with high sensitivity at single-nucleotide resolution.

Nature protocols·2026

Same journal

An assay to quantify sexual commitment and stage conversion in the human malaria parasite Plasmodium falciparum.

Nature protocols·2026

Same journal

Author Correction: Direct inoculation of bioreactor-controlled stirred suspension culture with cryopreserved human pluripotent stem cells.

Nature protocols·2026

Same journal

High-throughput measurements of protein domain functions using magnetic separation.

Nature protocols·2026

Same journal

Inducing physiological polarity and performing gene editing using CRISPR-Cas9 in human trophoblast organoids.

Nature protocols·2026

Same journal

Photocatalytic low-temperature defluorination of PTFE.

Nature protocols·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Aug 23, 2025

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

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

Published on: July 19, 2024

StarMap: a user-friendly workflow for Rosetta-driven molecular structure refinement.

Wolfgang Lugmayr^1,2,3,4,5, Vadim Kotov^1,2,3,4,5,6, Nikolaus Goessweiner-Mohr^1,2,3,4,5,7

¹University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.

Nature Protocols

|November 3, 2022

Summary

This summary is machine-generated.

StarMap simplifies refining 3D atomic models from cryogenic electron microscopy (cryo-EM) density maps. This tool integrates ChimeraX and Rosetta for efficient model building and validation, requiring only general computer skills.

More Related Videos

A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion

A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion

Published on: January 31, 2022

Author Spotlight: Optimizing Cryo-EM Analysis with CryoSieve for Enhanced Particle Selection Efficiency

Author Spotlight: Optimizing Cryo-EM Analysis with CryoSieve for Enhanced Particle Selection Efficiency

Published on: May 10, 2024

Related Experiment Videos

Last Updated: Aug 23, 2025

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

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

Published on: July 19, 2024

A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion

A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion

Published on: January 31, 2022

Author Spotlight: Optimizing Cryo-EM Analysis with CryoSieve for Enhanced Particle Selection Efficiency

Author Spotlight: Optimizing Cryo-EM Analysis with CryoSieve for Enhanced Particle Selection Efficiency

Published on: May 10, 2024

Area of Science:

Structural Biology
Biophysics
Computational Biology

Background:

Cryo-electron microscopy (cryo-EM) yields high-resolution density maps of macromolecules.
Building and refining 3D atomic models from cryo-EM maps is complex and labor-intensive.

Purpose of the Study:

To develop an accessible tool for refining atomic models into cryo-EM density maps.
To streamline the process of model building and validation for cryo-EM data.

Main Methods:

Integration of ChimeraX and Rosetta into a user-friendly interface called StarMap.
Utilizing Monte Carlo sampling, density-guided optimization, and Rosetta-based refinement.
Incorporating options for structural symmetry, local refinements, and independent model validation.

Main Results:

StarMap provides a straightforward workflow for refining structural models.
Analytical outputs like Fourier shell correlations and Z-scores facilitate model assessment.
The tool allows for identification of flexible regions and potential functional sites.

Conclusions:

StarMap simplifies atomic model refinement from cryo-EM data, reducing the need for extensive expertise.
The protocol is accessible to users with general computer skills, operating via a graphical interface.
Efficient model refinement and validation are achievable within a reasonable timeframe.