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 chemistry software Mac OS X. Products include ADF, Alchemy Symbols, Amino Acid Table Widget, Atomic Mac, AtVol, Beware of Molecules, BNDLst, The CCP4 Suite, ChemDraw, The Chemical Thesaurus, Chemistry 4-D Draw Pro, ChemLabNotebook, Chenomx NMR Suite, Cluster, CN3D, CNS, Columbus, CrystalDiffract, Crystal Maker, CrystMol, Dang, Deep View Swiss-Pdb Viewer, DiscoveryGate, DisSolver, EDEN, Elements, FreeSFP.

ADF

[url=http://www.scm.com/]ADF[/url] (pictured) is a Density Functional Theory (DFT) software package for computational quantum chemistry. It enables first-principles electronic structure calculations and is used by theoretical and computational chemists worldwide, both in industry and in academia. The ADF software consists of three main modules: the molecular program ADF, the periodic structure program BAND, and a graphical user interface for ADF. ADF and BAND are popular for studying transition metal and heavy-element compounds, as well as for molecular property predictions.

Alchemy Symbols

[url=http://www.deniart.com/]The Alchemy Symbols Series[/url] contains over 130 unique characters based on the cryptic symbols used by Alchemists in the middle-ages. Referred to as steganographic and spagyric signs, the series includes symbols representing metals, processes, instruments, weights, materials and spirits. The typefaces ship with both TrueType & Type 1 font formats.

Amino Acid Table Widget

[url=http://www.aborygen.com/]Aminio Acid Table Widget[/url] is a widget that displays basic information on amino acids.

Atomic Mac

[url=http://www.blackcatsystems.com/]The Atomic Mac[/url] is an electronic version of the periodic table of elements, with detailed physical and nuclear information included.

AtVol

[url=http://kinemage.biochem.duke.edu/]AtVol[/url] is an Unix-based utility that performs atomic volume calculations by separating each atom from neighboring atoms where their van der Waals spheres join and performs Monte Carlo integration to estimate the volume.

Beware of Molecules

[url=http://home.no/totlandsw/]Beware of Molecules[/url] is a small utility for calculating molecular weights. It also has a built in periodic table. It comes loaded with over a hundred compounds, and more can be added.

BNdLst

[url=http://kinemage.biochem.duke.edu/]BndLst[/url] is an Unix-based utility that reads a Protein DataBank (PDB) molecular structure file and for each atom prints a list of covalent and H-bonded neighboring atoms. It can be used to build scripts for processing atomic structures.

The CCP4 Suite

[url=http://www.ccp4.ac.uk/main.html#ccp4d]The CCP4 Suite[/url], often referred to as "CCP4," is a large set of stand-alone programs designed primarily for macromolecular X-ray crystallography. There are many programs in the suite that are of interest to anyone dealing with structures of macromolecules.

ChemDraw

[url=http://www.cambridgesoft.com/]ChemDraw[/url] features stereochemistry, atom numbering, structure and style templates, a variety of bonds and arrows, full color drawing, and more.

The Chemical Thesaurus

[url=http://www.meta-synthesis.com/]The Chemical Thesaurus[/url] is free reaction chemistry software for personal use.

Chemistry 4-D Draw Pro

[url=http://www.cheminnovation.com/]Chemistry 4-D Draw[/url] combines three components in a package: a drawing program, NamExpert, and Nomenclator. The program allows you to obtain high-quality structures by entering molecular names. It also assigns systematic names to structures according to IUPAC rules. The program includes a full set of tools for drawing and text editing.

ChemLabNotebook

[url=http://www.macinchem.fsnet.co.uk/]ChemLabNotebook[/url] is an electronic laboratory notebook for chemists. The notebook consists of two databases: the notebook itself and a built-in reagents database. 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. The notebook also provides links to Chemdraw for calculation of MWt, formula etc. Users can add 10 records you will then need a password to add further experiments.

Chenomx NMR Suite

[url=http://www.shpvt.com/]Chenomx NMR Suite[/url] is an integrated set of tools for identifying and quantifying metabolites in NMR spectra. By combining chemistry with advanced algorithms, Chenomx NMR Suite 4.5 offers a metabolic profiling platform.

Cluster

[url=http://kinemage.biochem.duke.edu/]Cluster[/url] is an Unix C++ utility that builds collections of interacting items from files containing interacting pairs or larger fragments.

CN3D

[url=http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml]CN3D[/url] is a helper application for your web browser that allows you to view 3-D structures from NCBI's Entrez retrieval service.

CNS

[url=http://cns.csb.yale.edu/v1.1/]Crystallography & NMR System (CNS)[/url] has been developed for macromolecular structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy. The architecture of CNS is flexible, allowing for extension to other structure determination methods, such as electron microscopy and solid state NMR spectroscopy.

Columbus

[url=http://homepage.univie.ac.at/hans.lischka/]Columbus[/url] s a collection of programs for high-level ab initio molecular electronic structure calculations. The programs are designed primarily for extended multi-reference (MR) calculations on electronic ground and excited states of atoms and molecules.

CrystalDiffract

[url=http://www.crystalmaker.com/]CrystalDiffract[/url] is a program for working with x-ray ad neutron powder diffraction crystals. It can simulate and visualize diffraction patterns from any CrystalMaker binary file. You can manipulate patterns in real time, with control over all aspects of the diffraction experiment. CrystalDiffract also offers the ability to edit site occupancies and lattice parameters. It lets you display multiple diffraction patterns (simulated and real) in the same window. Plus, you can simulate multi-phase mixtures (with variable phase proportions), plus energy-dispersive and time-of-flight diffraction.

Crystal Maker

[url=http://www.crystalmaker.com/]CrystalMaker[/url] is a program for building, displaying and manipulating all kinds of crystal and molecular structures with real-time photorealistic graphics and "out-of-the-screen" 3D display. It sports input/output capabilities, with support for major structural database formats, export of ultra-high resolution graphics, QuickTime movies and QTVR objects.

CrystMol

[url=http://www.crystmol.com/]CrystMol[/url] is a program that supports: the display, analysis, and manipulation of chemical structures represented as atoms and bonds in three-dimensions; the study of isolated molecules or crystal structures; analysis of all size structures from the smallest molecule to large macromolecules; the building of molecular models interactively in three dimensions; molecular mechanics calculations; the creation of QuickTime movie clips of structures; and more. It's designed for a wide variety of users, from the secondary school student learning about molecules for the first time, to the research scientist analyzing new molecular structures.

Dang

[url=http://kinemage.biochem.duke.edu/]Dang[/url] is a 3D graphics program which produces a table of geometric measurements from a Protein DataBank (PDB) molecular structure file.

Deep View Swiss-Pdb Viewer

[url=http://us.expasy.org/]Deep View Swiss-Pdb Viewer[/url] is a stand-alone application that lets you analyze several proteins simultaneously. It integrates with the Swiss-Model homology modeling serve and reads electron density maps.

DiscoveryGate

[url=http://www.mdl.com/]DiscoveryGate[/url] is a web-based discovery environment that integrates, indexes, and links scientific information to give you access to compounds and related data, reactions, original journal articles and patents, and authoritative reference works on synthetic methodologies.

DisSolver

[url=http://hoylab.cornell.edu/wytt/dissolver.html]DisSolver[/url] is an app for managing databases of chemicals and formulae. It's designed to automate exacting but tedious calculations.

EDEN

[url=http://www.mssm.edu/students/jovinl02/research/eden_osx.html]EDEN[/url] is an implementation of the holographic method to recover the electron density distribution of molecules within a crystal.

Elements

[url=http://digitalscience.free.fr/]Elements[/url] is a searchable periodic table of elements. Passing your mouse over an element give you access to general information. Clicking an element gives you full information, such as atomic structure, physical properties, electron configuration with graphical diagram and isotopes.

FreeSFP

[url=http://www.svi.nl/]FreeSFP[/url] is a free volume renderer that enables you to explore 3D digital images from a selectable viewpoint. It's developed by the makers of the Huygens deconvolution software (also available for Mac OS X). It's built for single or multi-channel images from microscopes or MRI. The computational work is done by the Simulated Fluorescence Process (SFP) algorithm that was developed and published by Dr. Hans van der Voort, founder and research & development director of SVI. FreeSFP takes the volume image as a distribution of fluorescent material, simulating what happens if the material is excited and how the subsequently emitted light travels to the observer.

Next week: part II

 

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