Software for CIT

This is a non-exhaustive list of software, including software that you will find on cluster PCs and other software available for you to install and use on your own computer. If there is anything you find useful, please add it to the list in the appropriate area, along with a brief description of what it does. If you find anything which is so useful you think it should be installed on the cluster computers, please do speak to either Professor Henry Rzepa or Dr. Andrew McKinley and we can investigate any possibilities.

Software listed by category

Spectroscopic software

gNMR5 - NMR simulation software
Mestrenova - NMR spectral analysis software
mMass - Mass spectrometry software
Spinworks 3 - NMR analysis software
Torganal - Spectroscopic training software

Molecular visualisation software

Avogadro - visualiser, multiplatform
Gaussview - viewer for Gaussian output
Mercury 2.3 - CCDC visualisation application
PyMOL tools - Molecular visualization system on an open-source foundation
VMD - Software for visualisation
wxMacMolPlt - Simple molecular display, visualisation of symmetries
Accelrys - Visualisation software
- Discovery Studio Visualiser
- DS Visualiser
- Accelrys Viewer lite
Hermes - Comprehensive Protein Visualiser
ChemBio3D Ultra - Molecular graphics and computational methods package
VMD - Visual Molecular Dynamics - for analysing large biomolecular systems

Data mining software

Conquest - Search the Cambridge Structural Database (CSD)
IsoStar Client - A Knowledge Base of Intermolecular Interactions
Mogul - A Knowledge Base of Molecular Geometry
Prequest - Creation of In-House Databases in CSD format
ChemBioFinder Std - A chemically and biologically intelligent database manager and search engine
Scifinder Scholar - Client software for SciFinder; redundant as of 2011

Drawing packages

ChemBioOffice 2010
- ChemBio3D Ultra - Molecular graphics and computational methods package
- ChemDraw Pro - Chemical structure drawing and more
DeLano Scientific
Gimp - The GNU Image Manipulation Program

Computational Chemistry Packages

Gold - program for calculating the docking modes of small molecules in protein binding sites
SuperStar - Predicting Protein-Ligand Interactions Using Experimental Data
Gabedit - A graphical user interface for computational chemistry packages

Gaussian 03W - Electronic structure modelling
Gaussian 09W - Electronic structure modelling
GaussView 5.0 - Visualisation of Gaussian output
MATLAB - Mathematical modelling and data analysis
OpenBabel - Toolbox to use different languages of chemistry data
VMD - Visual Molecular Dynamics - for analysing large biomolecular systems

Data Analysis software

GnuPlot - Graphing utility
MATLAB - Mathematical modelling and data analysis
OriginLab - Data analysis and graphing software

Education and learning software

gNMR5 - NMR simulation software
Torganal2 - Spectroscopy training software

Report writing tools

GnuPlot - Graphing utility
Microsoft Office
OpenOffice - Free alternative to Microsoft Office
ChemDraw Pro - Chemical structure drawing and more

Citation and document library software

Mendeley desktop - document library manager
Endnote - Citation management software
Refworks - Citation management - Free for IC students

Utilities

Adobe Reader 9 - PDF reader
PuTTy - command line TelNet SSH tool
XPS viewer - Tool for viewing XML files
Filezilla FTP - Free FTP software

Google Earth
iTunes
jDiskReport - Monitor hard disk space usage
Mozilla Firefox - Extensible web browser
OpenBabel - Toolbox to use different languages of chemistry data
PrimoPDF - Free PDF virtual printing software
Quicktime
RealPlayer
Winzip
Xming - X Window server for Windows

Software for Macintosh computers

Both Mendeley and ChemDraw 3D are available free for Macintosh computers. You can get ChemDraw 3D for free by using the free license provided by the college, see below.

Software for mobile devices

iOS devices

ChemSpider - [1]
Mendeley - [2]
WolframAlpha - [3]
RSC Mobile - Read the latest RSC papers on your device
ChemJuice - Excellent and easy to use molecular drawing program (there is a Grande version for iPad)
iMoleBuilder - Not so straightforward 3d drawing program, but good when you don't have your modelling kit handy
Molecules - 3d molecule viewing program, you can't draw but you can download molecules from PubChem or the Protein Data Bank, better than iMoleBuilder for more complex molecules

Android devices

(this needs expanding)

No official Mendeley client exists yet, but Droidely, Referey and Scholarley are third-party alternatives

Software installed on Chemistry Cluster Computers

Start menu items

Adobe Reader 9 - PDF reader
Avogadro - visualiser, multiplatform
ChemDraw Pro 2013 - ChemDraw
Conquest - accessing Cambridge Structure DataBase
Database of NMR Spectra - NMR Predictor
Discovery Studio 3.5 Client - Discovery studio Visualiser
Gabedit - GUI for various computational chemistry programs
Gaussian 09 - Molecular modelling
Gaussview 5.0 - viewer for Gaussian output
GIMP 2 - Photo editor
gNMR5 - NMR simulation software
Lyx 2.0 - Document processing
MATLAB R2013a - Maths
Mendeley desktop - document library manager
Mercury 2.3 - CCDC visualisation application
Mestrenova - NMR spectral analysis software
mMass - Mass spectrometry software
Mozilla Firefox - web browser
OpenBabel - translates molecular file formats
OpenOffice 4.0.0 - free alternative to MS Office
OriginPro 9 - data analysis and graphing
Paint.net - image editor
PyMOL - Molecular graphics software
reaxys - shortcut
Scifinder - shortcut
Spinworks 3 - NMR analysis software
Torganal - Spectroscopic training software
VMD - Software for visualisation
wxMacMolPlt - Simple molecular display, visualisation of symmetries
XPS viewer - Tool for viewing XML files

Start menu folders

Accelrys - Visualisation software
- Discovery Studio Visualiser
- DS Visualiser
- Accelrys Viewer lite
CCDC - Software from the Cambridge Crystallographic Data Centre
- CSD System Software -> Mercury
- CSD System Software 2011
  - Conquest - Search the Cambridge Structural Database (CSD)
  - IsoStar Client - A Knowledge Base of Intermolecular Interactions
  - Mercury - Crystal Structure Visualisation
  - Mogul - A Knowledge Base of Molecular Geometry
  - Prequest - Creation of In-House Databases in CSD format
- Gold Suite
  - Gold - program for calculating the docking modes of small molecules in protein binding sites
  - Hermes - Comprehensive Protein Visualiser
- SuperStar - Predicting Protein-Ligand Interactions Using Experimental Data
ChemBioOffice 2010
- ChemBio3D Ultra - Molecular graphics and computational methods package
- ChemBioFinder Std - A chemically and biologically intelligent database manager and search engine
- ChemDraw Pro - Chemical structure drawing and more
DeLano Scientific
- PyMOL tools - Molecular visualization system on an open-source foundation
Endnote - Citation managment software
Filezilla FTP - Free FTP software
Gabedit - A graphical user interface for computational chemistry packages
Gaussian 03W - Electronic structure modelling
Gaussian 09W - Electronic structure modelling
GaussView 5.0 - Visualisation of Gaussian output
Gimp - The GNU Image Manipulation Program
GnuPlot - Graphing utility
Google Earth
iTunes
jDiskReport - Monitor hard disk space usage
MATLAB - Mathematical modelling and data analysis
Microsoft Office
Mozilla Firefox - Extensible web browser
OpenBabel - Toolbox to use different languages of chemistry data
OpenOffice - Free alternative to Microsoft Office
OriginLab - Data analysis and graphing software
PrimoPDF - Free PDF virtual printing software
Quicktime
RealPlayer
Refworks - Citation management - Free for IC students
Scifinder Scholar - Client software for SciFinder; redundant as of 2011
Torganal2 - Spectroscopy training software
University of Illinois
- VMD - Visual Molecular Dynamics - for analysing large biomolecular systems
Winzip
Xming - X Window server for Windows

Other useful software

Software licensing

Software packages are available under a large range of licenses, varying between licenses that are free of charge up to those which cost a great deal. For some software the department has a site license which allows the software to be used on any computer installed in the department, other software is licensed on a per seat basis, meaning that it may not be installed on every computer.

In general, as undergraduate students, you are not permitted to run software on your own computer under any site license held by the Department or the College as a whole. There are two exceptions to this:

ChemBio3D, including ChemDraw Pro. To register for a serial number visit this page
Norton anti-virus software

Both of these packages can be installed onto your personal computer at no cost to yourself.

Free software

The following list of software can be used to prepare reports and coursework, and are available at no charge for academic use (and in some cases are free of charge for general use!).

Note: Some software is free of charge, however the online service required to use them may not be; in these cases, unless there is a degree of 'free' access to the online service, the software is not included on this list.

OpenOffice.org - Free alternative to Microsoft Office. Can produce MSOffice compatible files, but take care with formatting between the two systems.
LaTeX (pronounced Lah-Tek) - A full typesetting system; documents are coded in a markup language (similar to HTML) and run through a processor to generate the finished document. Highly customisable, produces publication quality results, however steep learning curve. Excellent for formatting mathematical equations.
Mendeley - Document library software - library stored online, free for limited use; more storage incurs a charge.
Filezilla FTP - program for uploading files to a web server or transferring between servers.