MacNews Category Review: chemistry software for the Mac, part II
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MacNews Category Review: chemistry software for the Mac, part II

imageThis MacNews Category Review looks at part two of our round-up of chemistry software Mac OS X. Products include GelEval, iMass, iMoi, JChem Base, JMol, jVisualizer, KING, Lab Notebook, Mac the Scope, MacGAMESS, MacMoiPot, MacPyMOL, Mage, Marvin, Model ChemLab, Modeller, MOE, Molconn-z, Molden, Mlegro Virtual Docker, MOLMOL, MolScript, MolView X, MOSFLM, NAMD, Nucleic Acid Nomenclature Widget, OEChem, OMA, OpenBabel, PDB to MultiGIF, Periodic Table, PLS Toolbox, Prekin, Probe and PyMOL Molecular Graphics System.

Gaussian 03M

[url=http://www.gaussian.com/]Gaussian 03M[/url] is used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical interest. Starting from the basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds.

GaussViewM is a graphical user interface for Gaussian. With GaussViewM you can construct molecular systems using its molecule building facility. You can also use it to set up and run Gaussian calculations and to visualize a variety of results. GaussViewM incorporates a molecule builder for building large molecules.

GelEval

[url=http://www.frogdance.dundee.ac.uk/]GelEval[/url] (shown above) is a software tool for quantifying electrophoresis gels. It can measure the densities of individual gel bands and can show the changing density along individual gel lanes. Starting from the scanned image of a gel, GelEval allows you to delimit the boundaries of individual bands and/or lanes. The total density of individual bands can then be measured. If your gel contains known standards, line-fitting is applied to express band intensity relative to the standards. Alternatively, lanes can be scanned to give a graphical representation of intensity as you move from top to bottom of the delimited region.

iMass

[url=http://home.datacomm.ch/marvin/iMass/]iMass[/url] (short for isotopeMass) includes a molecular mass calculator, a periodic table of the elements, an isotope distribution graph and a calculator that computes elemental compositions matching a given mass. It "understands" complex chemical formulas as well as user defined abbreviations for commonly used formulas.

iMol

[url=http://www.pirx.com/]iMol[/url] is a free molecular visualization application that allows loading molecules using several file formats: PDB, MOL2, HIN, CAR, ALC, XYZ, BIO. It can handle both small and large molecules and can load multiple molecules, move and rotate them independently. iMol uses OpenGL graphics to display molecules. The molecules can be rendered using various styles. Individual atoms and/or residues can be selected and rendered independently. There are several predefined color schemes available, as well as custom colors. The rendered images can be exported as a bitmap, as a PostScript file, or as a POV-Ray file. The program can measure distances, angles, and torsional angles between atoms. Molecules can be superimposed and RMSD between atom coordinates can be calculated. Additionally, protein chains can be structurally aligned to detect regions of high structural similarity. iMol can load multimodel PDB files and display them as a dynamics trajectory.

JChem Base

[url=http://www.chemaxon.com/]JChem Base[/url] is a Java tool for the development of applications that allow for the search of mixed chemical structure and non-structural data and can integrate a variety of database systems (Oracle, SQL, Access, etc) with web interfaces. The system includes Marvin, a substructure, similarity, and exact search engine using 2D hashed fingerprints. Structures are stored in database tables and SDF, SMILES, SMARTS, etc. can be imported and exported.

JMol

[url=http://jmol.sourceforge.net/]JMol[/url] is a free, open source molecule viewer. It is a collaboratively developed visualization and measurement tool for chemical scientists.

jVisualizer

[url=http://jvisualizer.sourceforge.net/]jVisualizer[/url] is software for analysis and visualisation of first order NMR coupling patterns.

KiNG

[url=http://kinemage.biochem.duke.edu/]KiNG[/url] is a 3D interactive vector graphics program that uses the kinemage input format. It's a Java application with integrated editing functions and was designed primarily to display macromolecular structures.

Lab Notebook

[url=http://www.macinchem.fsnet.co.uk/]Lab Notebook[/url] is an electronic laboratory notebook for chemists. The notebook consists of two databases: the notebook itself and a reagents database. It automates calculations, stores safety information, spectral data and more. The reagents database contains the structures, name, MWt, density and safety information on over 13,000 compounds that can be used as reagents. Entering the name of a reagent into the notebook causes the rest of the information to be "looked up" from the reagents database.

Mac the Scope

[url=http://www.channld.com/prdinf.html]Mac the Scope[/url] comprises an audio signal generator, vector FFT analyzer, sonogram display, time domain RTA and more.

MacGAMESS

[url=http://www.msg.ameslab.gov/GAMESS/dist.mac.html]MacGAMESS[/url] is a fully functional sequential implementation of GAMESS (General Atomic and Molecular Electronic Structure System).

MacMolPit

[url=http://www.scl.ameslab.gov/~brett/MacMolPlt/]MacMolPit[/url] is a program for plotting 3-D molecular structures and normal modes (vibrations).

MacPyMOL

[url=http://www.delanoscientific.com/]MacPyMOL[/url] is a special version of the PyMOL Molecular Graphics System, enhanced for Aqua and Mac OS X. PyMOL is the open-source molecular graphics system based on the Python scripting language. In addition to including all of the features of Open-Source PyMOL, MacPyMOL also supports direct copy and paste of molecular images into other programs and direct QuickTime movie export.

Mage

[url=http://kinemage.biochem.duke.edu/]Mage[/url] is a 3D interactive graphics program using the kinemage input format. It originated and is maintained primarily as a macromolecular structure viewing utility for research and teaching, though it's also used for visualizing 3D social and ecological networks.

Marvin

[url=http://www.chemaxon.com/]Marvin[/url] is a collection of Java tools for drawing, displaying and characterizing chemical structures, substructures and reactions. These applets and beans can be implemented in applications to allow users to create, edit, view and process chemical structures offline or over the web.

Model ChemLab

[url=http://modelscience.com/]Model ChemLab[/url] is an interactive simulation of a chemistry lab. Commonly used lab equipment and procedures are employed to simulate the steps involved in performing a chemistry lab experiment.

Modeller

[url=http://salilab.org/modeller/]Modeller[/url] is used for homology or comparative modeling of protein three-dimensional structures. You provide an alignment of a sequence to be modeled with known related structures and Modeller automatically calculates a model containing all non-hydrogen atoms. It implements comparative protein structure modeling by satisfaction of spatial restraints and can perform several additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, and more.

MOE

[url=http://www.chemcomp.com/]MOE (Molecular Operating Environment)[/url] is a software package for the life science marketplace, combining High Throughput Discovery, Bioinformatics and Computer Aided Molecular Design.

Molconn-z

[url=http://www.edusoft-lc.com/]Molconn-ZTM[/url] is a text/keyword-driven program designed to cleanly produce formatted output that, in turn, can be imported into sophisticated statistical packages like SAS. It produces a large collection of non-empirical structure-based parameters useful for QSAR and other computational chemistry technologies.

Molden

[url=http://www.cmbi.ru.nl/molden/molden.html]Molden[/url] is a package for displaying molecular density.

Molegro Virtual Docker

[url=http://www.molegro.com/]Molegro Virtual Docker[/url] is an integrated software platform for drug discovery using molecular docking. It handles all aspects of the molecular docking process from preparation of the molecules to determination of the potential binding sites of the target protein, and prediction of the binding modes of the ligands.

MOLMOL

[url=http://129.132.45.141/wuthrich/software/molmol/]MOLMOL[/url] is software that analyses, manipulates and displays 3D structures of biological macromolecules.

MolScript

[url=http://www.avatar.se/]MolScript[/url] is an application for displaying 3D molecular structures.

MolView X

[url=http://www.danforthcenter.org/smith/molview.htm]MolViewX[/url] can read several types of coordinate files and display ribbon, CPK, stick, ball&stick, and surface figures. The interface is interactive. There are options that control the display colors and characteristics. The output includes object-oriented PICT, VRML, and QuickDraw 3D 3DMF files. In addition, there are several analysis tools such as neighbors, distance lines, hydrophathy plots, Edmunson wheel plots, B value plots (and color coded stick models), distance plots.

MOSFLM

[url=http://www.mrc-lmb.cam.ac.uk/harry/frames/]MOSFLM[/url] is a a program for integrating single crystal diffraction data from area detectors. It is assumed that the experiment was conducted using the Arndt-Wonacott oscillation method, and also that monochromatic radiation was used.

NAMD

[url=http://www.ks.uiuc.edu/Research/namd/]NAMD[/url] is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. It scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using switched fast Ethernet.

Nucleic Acid Nomenclature Widget

[url=http://www.aborygen.com/]Nucleic Acid Nomenclature Widget[/url] is a widget that displays basic info on nucleic acids.

OEChem

[url=http://www.eyesopen.com/]OEChem[/url] is a programming library for Chemistry and Chemical Informatics.

OMA

[url=http://oma-x.org/]OMA (Optical Multi-Channel Analyzer)[/url] was developed by researchers as a way to investigate and post-process photometric images from CCD detectors used for laser-based imaging of reacting and nonreacting flows as well as for some spectroscopic applications. It includes processing routines for particle image velocimetry (PIV) and has macro scripting capabilities. The full source code is available.

OpenBabel

[url=http://openbabel.sourceforge.net/wiki/]OpenBabel[/url] is a cross-platform program and library designed to inter-convert between file formats used in molecular modeling and computational chemistry.

PDB to MultiGIF

[url=http://www.dkfz-heidelberg.de/spec/pdb2mgif/]PDB to MultiGIF[/url] is a utility to facilitate web viewing of 3D chemical structures. It makes animated GIFs of PDB files.

Periodic Table

[url=http://www.synergycreations.com/]Periodic Table[/url] is designed as a quick reference tool for high school and college students in introductory chemistry courses, along with anyone else who needs a quick periodic table reference.

PLS Toolbox

[url=http://www.eigenvector.com/]PLS Toolbox[/url] is a collection of essential and advanced chemometric routines, such as methods for analyzing data from chemical applications. This includes multivariate analysis routines such as Principal Components Analysis (PCA) and calibration methods such as Partial Least Squares (PLS) Regression, for which the toolbox is named. PLS Toolbox also includes an advanced collection of multi-way analysis methods.

Prekin

[url=http://kinemage.biochem.duke.edu/]Prekin[/url] is a 3D graphics program that prepares molecular kinemages from Protein DataBank (PDB) formatted coordinate files. It can be used interactively or run in command-line function.

Probe

[url=http://kinemage.biochem.duke.edu/]Probe[/url] is a 3D graphics program that evaluates atomic packing in molecules by generating "contact dots" of the atoms using the kinemage format.

PyMOL Molecular Graphics System

[url=http://www.delanoscientific.com/]PyMOL[/url] is a Python-enhanced cross-platform molecular graphics program. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. PyMOL also includes molecular editing, ray tracing, and movies.

 

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