Categories Desktop Apps For You

Jmol

Name: Jmol
Rating: 5 (5 reviews)

14.30.0

27 November 2019

Molecule viewer for students/educators/researchers.

Overview

Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry.

Cross-platform, running on Windows, OS X, and Linux/Unix systems.
The JmolApplet is a Web browser applet that can be integrated into Web pages.
The Jmol application is a standalone Java application that runs on the desktop.
The JmolViewer is a development tool kit that can be integrated into other Java applications.

What's new in Jmol

Version 14.30.0:

New feature: set minimizationMaxAtoms maximum number of atoms allowed for MMFF minimization defaults to 200
New feature: MEASURE SEARCH "{[H]}CC{[H]}" uses SMARTS searching, selecting only the specified atoms actually available but undocumented since 2013
New feature: SET MEASUREMENTUNITS HZ for example, set measurementUnits HZ; MEASURE SEARCH "{[H]}CC{[H]}" will display all 1H-1H coupling constants for a model display calculated three-bond (standard vicinal) H-H J coupling constants (SMARTS {[H]}CC{[H]}) calculated using Haasnoot-Altona-Karplus substituent electronegativity-adjusted algorithm instead of distances
If there are fewer than three substituents on each central atom, or if either central atom is not carbon, defaults to general Karplus equation. see org.jmol.quantum.NMRCalculation.java for algorithm and bibliographic details expanded from use in solid-state NMR to any model EXCEPT magres files, which instead use HZ in associationg with solid-state tensors
New feature: SET MEASUREMENTUNITS NOE_HZ adds NOE calculation for H atoms that are more then three bonds apart along with vicinal and geminal not validated; from Janocchio 1.1 (https://sourceforge.net/projects/janocchio/)
New feature: Janocchio application included as a plugin (preliminary)
Java only; totally experimental; VERY preliminary org.openscience.jmol.app.janocchio required some refactoring of Jmol app classes commit number 22001!
New feature: LOAD ... CENTROID for molecular crystal structures
loads one or more unit cells (as specified by {nx ny nz}) exploring covalent bonding so that molecules that have their centroid (center of geometry) within the specified block of cells are built. available but undocumented since 2011 example: load =cod/1001253 {1 1 1} centroid note that {1 1 1} here is unnecessary, as it is the default
Bug fix: "DOMReader" not "DOMReadaer" in File Manager