From owner-chemistry ":at:" ccl.net Fri Jun 13 03:09:01 2008
From: "Vlad vvv900__anusf.anu.edu.au" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL:G: Java Molecular Editor 08 Released
Message-Id: <-37150-080613030313-28367-BZ3ZruyQLjACxJ1vDIoyRw * server.ccl.net>
X-Original-From: Vlad <vvv900-$-anusf.anu.edu.au>
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Date: Fri, 13 Jun 2008 15:26:01 +1000
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Sent to CCL by: Vlad [vvv900- -anusf.anu.edu.au]
Dear CCLers,

We are pleased to announce the release of Java Molecular Editor (JMolEditor) 08.

Java Molecular Editor (JMolEditor) is a program for displaying, analyzing, editing, and converting molecular systems. JMolEditor 
is written in Java, so it is a cross-platform application.

It has intuitive interface and inbuilt help system. JMolEditor can be used also for the analysis to display molecular orbitals, 
electron densities and electrostatic potentials from the Gaussian.

A full description of JMolEditor and its documentation are available via the JMolEditor WWW home page: 
http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html

System requirements: Java Virtual Machine (JVM) >= 1.5 and Java3d >= 1.4.

Key features in JMolEditor include:

- Molecular builder/editor
- - (http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/manual/editing-molecule/index.html)

- Ability to read and visualize popular Computational Chemistry formats
- - (http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/input-files.html):
- - Gaussian (input, output, cube, fragment, trajectory)
- - ADF (input, output)
- - Gamess (input and output)
- - Mopac (input and output)
- - QChem (input and output)
- - VASP (input, vasprun.xml)
- - Amber (prmtop files)
- - Gromacs  (gro files)
- - GULP (input)
- - Siesta input (in development)
- - PDB, Tripos Mol2, MDL molfile, XMol XYZ

- Output
- - Gaussian input
- - XMol XYZ
- - Tripos Mol2
- - PDB
- - Povray

- Visualization of the OOGL off files

- Ability to load and visualize Computational Chemistry files from SFTP server

- Visualization of molecular orbitals, electron densities, electrostatic potentials and mapped surfaces from the Gaussian Cube 
files

- Interactive Charting
- - (http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/manual/charting/index.html)
- - ability to display plots of energy and other quantities from calculations that produce multiple structures among their results
- - ability to interact with a plot to view corresponding structure
- - supported formats: gaussian and ADF output, Vasprun.xml files

-  Vibrational Analysis
- - http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/manual/frequencies/index.html
- - ability to display various spectra (Infrared, Raman, etc.) based on information from Gaussian frequency calculation
- - ability to animate vibrations for selected frequency
- - ability to show displacement vectors for selected frequency

- Tools
- - In-built SFTP browser (http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/manual/sftp-browser/index.html)

- Tutorials
- - Gaussian (http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/manual/tutorials/index.html)

Future plans include support of periodic/crystal structures, writing documentation and tutorials, interfaces to additional 
computational packages, etc.

JMolEditor is also a free, open source, cross-platform Computational Chemistry Toolkit which could be extended and/or used in 
other applications. Source code is provided under the Apache2, GPL, and LGPL licenses 
(http://sf.anu.edu.au/~vvv900/cct/api/index.html). So, the developers who like challenge and aggressive programming are welcome 
to contribute.

Regards,
Vlad
===============

Dr. Vladislav Vasilyev
Supercomputer Facility
The Australian National University
Canberra, ACT, 0200, Australia