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

Preparation of Samples for Electron Microscopy01:20

Preparation of Samples for Electron Microscopy

To be visualized by an electron microscope, either transmission or scanning, biological samples need to be fixed (stabilized) so the electron beam does not destroy them and dried thoroughly (desiccated/dehydrated) so the vacuum does not affect them. Fixation needs to be done as quickly as possible because the sample properties will start changing as soon as it is removed from its natural environment. For example, in a tissue sample, the oxygen levels begin decreasing, causing an altered...
Fixation and Sectioning01:03

Fixation and Sectioning

Two basic types of preparation are used to visualize specimens with a light microscope: wet mounts and fixed specimens.
The simplest type of preparation is the wet mount, in which the specimen is placed in a drop of liquid on the slide. A liquid specimen can be directly deposited on the slide using a dropper. Solid specimens, such as skin scraping, can be placed on the slide before adding a drop of liquid to prepare the wet mount. Sometimes the liquid is simply water, but stains are often added...

You might also read

Related Articles

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

Sort by
Same author

RNAprecis: Prediction of full-detail RNA conformation from the experimentally best-observed sparse parameters.

PLoS computational biology·2026
Same author

New targets and procedures for validating the valence geometry of nucleic acid structures.

Nucleic acids research·2026
Same author

Categorizing prediction modes within low-pLDDT regions of AlphaFold2 structures: near-predictive, pseudostructure and barbed wire.

Acta crystallographica. Section D, Structural biology·2025
Same author

Categorizing prediction modes within low-pLDDT regions of AlphaFold2 structures.

bioRxiv : the preprint server for biology·2025
Same author

Cis-nonProline peptides: Genuine occurrences and their functional roles.

Protein science : a publication of the Protein Society·2025
Same author

RNAprecis: Prediction of full-detail RNA conformation from the experimentally best-observed sparse parameters.

bioRxiv : the preprint server for biology·2025

Related Experiment Video

Updated: May 18, 2026

Studying Dynamic Processes of Nano-sized Objects in Liquid using Scanning Transmission Electron Microscopy
10:29

Studying Dynamic Processes of Nano-sized Objects in Liquid using Scanning Transmission Electron Microscopy

Published on: February 5, 2017

Studying and polishing the PDB's macromolecules.

Jane S Richardson1, David C Richardson

  • 1Department of Biochemistry, Duke University, Durham, North Carolina, USA. jsr@kinemage.biochem.duke.edu

Biopolymers
|October 2, 2012
PubMed
Summary
This summary is machine-generated.

Macromolecular crystal structures offer valuable data but require improved evaluation of model reliability and 3D visualization tools. Enhancing molecular 3D literacy is crucial for better scientific inference from Protein Data Bank (PDB) data.

More Related Videos

Microfluidic Mixers for Studying Protein Folding
12:42

Microfluidic Mixers for Studying Protein Folding

Published on: April 10, 2012

Chemotactic Response of Marine Micro-Organisms to Micro-Scale Nutrient Layers
22:38

Chemotactic Response of Marine Micro-Organisms to Micro-Scale Nutrient Layers

Published on: May 28, 2007

Related Experiment Videos

Last Updated: May 18, 2026

Studying Dynamic Processes of Nano-sized Objects in Liquid using Scanning Transmission Electron Microscopy
10:29

Studying Dynamic Processes of Nano-sized Objects in Liquid using Scanning Transmission Electron Microscopy

Published on: February 5, 2017

Microfluidic Mixers for Studying Protein Folding
12:42

Microfluidic Mixers for Studying Protein Folding

Published on: April 10, 2012

Chemotactic Response of Marine Micro-Organisms to Micro-Scale Nutrient Layers
22:38

Chemotactic Response of Marine Micro-Organisms to Micro-Scale Nutrient Layers

Published on: May 28, 2007

Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Macromolecular crystal structures are high-quality scientific data.
  • Challenges exist in evaluating model reliability and interpreting complex 3D molecular interactions.
  • Protein Data Bank (PDB) is a vital resource for structural data.

Purpose of the Study:

  • To address limitations in interpreting macromolecular crystal structures.
  • To improve the evaluation of local reliability in structural models.
  • To enhance 3D literacy for understanding complex molecular structures and functions.

Main Methods:

  • Review of historical involvement with Protein Data Bank (PDB) data.
  • Analysis of methods for evaluating structural model quality.
  • Development of graphical representations and descriptive classifications for molecular structures.

Main Results:

  • Identified needs for improving macromolecular structure models.
  • Highlighted the importance of assessing local reliability for scientific questions.
  • Emphasized the necessity of tools for intuitive understanding of molecular 3D structures.

Conclusions:

  • Improved methods are needed to fully leverage macromolecular crystal structure data.
  • Enhanced 3D visualization and reliability assessment are key for scientific discovery.
  • Continued development of tools and classifications will advance molecular 3D literacy.