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

Determination of Crystal Structures01:29

Determination of Crystal Structures

118
In the late 1800s, the revelation that light extended beyond visible wavelengths led to the discovery of X-rays by Wilhelm Roentgen. Recognized as high-energy electromagnetic radiation with short wavelengths, X-rays prompted exploration into their interaction with crystals. Max von Laue proposed in 1912 that the periodic arrangement of atoms, ions, or molecules in crystals would cause them to diffract X-rays, a hypothesis confirmed through experiments with copper sulfate and zinc sulfide...
118
High-Resolution Mass Spectrometry (HRMS)01:15

High-Resolution Mass Spectrometry (HRMS)

2.9K
The resolution of a mass spectrometer depends on the efficiency of separating ions with different ion masses. The mass of an atom is approximated to the sum of the masses of protons and neutrons inside, considering the masses of protons and neutrons as equal. However, the masses of the proton (1.6726 × 10−24 g) and neutron (1.6749 × 10−24 g) are not truly equal. There is a minor error in the expression of atomic masses relative to the simplest atom of hydrogen. For...
2.9K
Mass Spectrum: Interpretation01:24

Mass Spectrum: Interpretation

4.4K
An unknown compound can be established by identifying the molecular ion peak in the mass spectrum. The molecular ion peak is often weak or absent due to the predominance of fragmentation in high-energy electron beams. In such cases, a soft-energy electron beam can be used to scan the spectrum to enhance the intensity of the molecular ion peak. Additionally, chemical ionization, field ionization, and desorption ionization spectra are used to obtain a relatively intense molecular ion peak.To...
4.4K
Electrospray Ionization (ESI) Mass Spectrometry01:12

Electrospray Ionization (ESI) Mass Spectrometry

2.9K
Higher molecular weight biomolecules are nonvolatile compounds that may decompose before ionizing or vaporizing during mass analysis with conventional electron impact ionization methods. Accordingly, electrospray ionization (ESI) is the favored method for vaporizing and ionizing biomolecules as it circumvents rapid fragmentation and enables the recording of mass signals for the entire biomolecule.
ESI utilizes electrical energy to transfer ions from the liquid phase of the sample into the...
2.9K
Ionic Crystal Structures02:42

Ionic Crystal Structures

21.4K
Ionic crystals consist of two or more different kinds of ions that usually have different sizes. The packing of these ions into a crystal structure is more complex than the packing of metal atoms that are the same size.
Most monatomic ions behave as charged spheres, and their attraction for ions of opposite charge is the same in every direction. Consequently, stable structures for ionic compounds result (1) when ions of one charge are surrounded by as many ions as possible of the opposite...
21.4K

You might also read

Related Articles

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

Sort by
Same author

iAstrocytes model cytokine influences on complement expression and neuronal network synchronization.

bioRxiv : the preprint server for biology·2026
Same author

Diversity-driven biochemical survey reveals widespread dimerization throughout the rubisco superfamily.

Nature communications·2026
Same author

The NMR Exchange Format (NEF): Specification and Applications.

bioRxiv : the preprint server for biology·2026
Same author

<i>pyDiSCaMB</i>: enabling the use of multipolar scattering factors in <i>Phenix</i>.

Journal of applied crystallography·2026
Same author

Variable Resolution Maps (VRM) in CCTBX and Phenix: Accounting For Local Resolution In cryoEM.

bioRxiv : the preprint server for biology·2026
Same author

Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields.

Acta crystallographica. Section D, Structural biology·2026

Related Experiment Video

Updated: Apr 13, 2026

Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides
11:04

Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides

Published on: September 7, 2019

10.0K

Using support vector machines to improve elemental ion identification in macromolecular crystal structures.

Nader Morshed1, Nathaniel Echols2, Paul D Adams2

  • 1College of Letters and Science, University of California, Berkeley, CA 94720, USA.

Acta Crystallographica. Section D, Biological Crystallography
|May 7, 2015
PubMed
Summary

Support vector machines (SVMs) automatically distinguish elemental ions from water molecules in protein structures. This method enhances crystallographic model building by accurately identifying metal ions and solvent sites.

Keywords:
elemental ion identificationmodel buildingsupport vector machines

More Related Videos

Sample Preparation and Transfer Protocol for In-Vacuum Long-Wavelength Crystallography on Beamline I23 at Diamond Light Source
10:32

Sample Preparation and Transfer Protocol for In-Vacuum Long-Wavelength Crystallography on Beamline I23 at Diamond Light Source

Published on: April 23, 2021

3.3K
Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092
08:53

Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092

Published on: October 2, 2017

32.0K

Related Experiment Videos

Last Updated: Apr 13, 2026

Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides
11:04

Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides

Published on: September 7, 2019

10.0K
Sample Preparation and Transfer Protocol for In-Vacuum Long-Wavelength Crystallography on Beamline I23 at Diamond Light Source
10:32

Sample Preparation and Transfer Protocol for In-Vacuum Long-Wavelength Crystallography on Beamline I23 at Diamond Light Source

Published on: April 23, 2021

3.3K
Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092
08:53

Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092

Published on: October 2, 2017

32.0K

Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Chemistry

Background:

  • Macromolecular model building requires distinguishing elemental ions from structured solvent molecules in electron density maps.
  • Accurate identification of ions is crucial but challenging due to complex metal-binding chemistry and scattering properties.
  • Previous methods relied on manual criteria, which are prone to errors and limited in scope.

Purpose of the Study:

  • To develop and validate a computational method using support vector machines (SVMs) for the automated classification of isolated atoms in crystallographic data.
  • To differentiate between solvent molecules (water) and various elemental ions.
  • To improve the accuracy and efficiency of macromolecular model building.

Main Methods:

  • Construction of two distinct datasets: manually curated protein crystal structures with anomalous diffraction data, and automatically filtered, high-resolution structures.
  • Training and application of support vector machine (SVM) classifiers on these datasets to distinguish between different elemental ions and water molecules.
  • Validation of the SVM models on independent test sets to assess classification accuracy.

Main Results:

  • SVM classifiers accurately distinguished calcium from manganese, zinc, iron, and nickel in the manually curated dataset.
  • The SVMs successfully differentiated these five metal ions from water molecules with high accuracy.
  • Models trained on automatically curated, high-resolution structures demonstrated successful classification of common elemental ions in independent validation tests.

Conclusions:

  • Support vector machines provide an effective automated approach for classifying elemental ions and solvent molecules in macromolecular structures.
  • This computational method enhances the accuracy and reduces errors in crystallographic model building.
  • The SVM approach is extensible to a wider range of elemental ions and can complement existing identification strategies.