MacNews Category Review: chemistry software for the Mac, part II
TweetFollow Us on Twitter

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.

 

Community Search:
MacTech Search:

Software Updates via MacUpdate

VirtualBox 5.1.10 - x86 virtualization s...
VirtualBox is a family of powerful x86 virtualization products for enterprise as well as home use. Not only is VirtualBox an extremely feature rich, high performance product for enterprise customers... Read more
Pixa 1.1.9 - Quickly and easily organize...
Pixa is an image-organizing application. The new app functions well, is easy to use, and helps people organize their images quickly and easily on their computers. For those who prefer not to use the... Read more
Civilization VI 1.0.1 - Next iteration o...
Sid Meier’s Civilization VI is the next entry in the popular Civilization franchise. Originally created by legendary game designer Sid Meier, Civilization is a strategy game in which you attempt to... Read more
Google Chrome 55.0.2883.75 - Modern and...
Google Chrome is a Web browser by Google, created to be a modern platform for Web pages and applications. It utilizes very fast loading of Web pages and has a V8 engine, which is a custom built... Read more
Chromium 55.0.2883.75 - Fast and stable...
Chromium is an open-source browser project that aims to build a safer, faster, and more stable way for all Internet users to experience the web. Version 55.0.2883.75: Security fixes: High CVE-2016... Read more
Luminar 1.0.2 - Powerful, adaptive, conf...
Luminar is the new full-featured image editor that adapts to the way you edit photos. Over 300 essential tools to fix, edit, and enhance your photos with comfort. The future of photo editing is here... Read more
Slack 2.3.3 - Collaborative communicatio...
Slack is a collaborative communication app that simplifies real-time messaging, archiving, and search for modern working teams. Version 2.3.3: Fixed window zoom jumping back-and-forth OS X 10.9... Read more
WhatRoute 2.0.10 - Geographically trace...
WhatRoute is designed to find the names of all the routers an IP packet passes through on its way from your Mac to a destination host. It also measures the round-trip time from your Mac to the router... Read more
Luminar 1.0.2 - Powerful, adaptive, conf...
Luminar is the new full-featured image editor that adapts to the way you edit photos. Over 300 essential tools to fix, edit, and enhance your photos with comfort. The future of photo editing is here... Read more
WhatRoute 2.0.10 - Geographically trace...
WhatRoute is designed to find the names of all the routers an IP packet passes through on its way from your Mac to a destination host. It also measures the round-trip time from your Mac to the router... Read more

Latest Forum Discussions

See All

Amateur Surgeon 4 Guide: Become the worl...
It's time to wield your trusty pizza cutter again, as Amateur Surgeon has returned with a whole fresh set of challenges (and some old, familiar ones, too). Starting anew isn't easy, especially when all you have at your disposal is a lighter, the... | Read more »
Le Parker: Sous Chef Extraordinaire (Ga...
Le Parker: Sous Chef Extraordinaire 1.0 Device: iOS Universal Category: Games Price: $2.99, Version: 1.0 (iTunes) Description: | Read more »
Telltale Games really is working on a Gu...
Telltale Games' next episodic adventure is indeed Guardians of the Galaxy. A document tied to the voice actors strike suggested that the project was in the work, but now we have direct confirmation following an announcement at the Game Awards that... | Read more »
Amateur Surgeon returns to iOS and Andro...
Amateur Surgeon and its two sequels disappeared from the App Store some time and it was sad days for all. But now, just in time for the holidays, the Adult Swim favorite makes its joyous return in the shape of Amateur Surgeon 4, a remake with... | Read more »
The best board games on mobile
Sometimes you need to ditch all of the high speed, high action games in favor of something a little more traditional. If you don't feel like parting ways from your mobile device, though, there are still plenty of ways to get that old-school fix.... | Read more »
The best Facebook Messenger Instant Game...
Facebook's new Instant Games is now here, meaning you can play games with your friends directly via Facebook. It's a fun new way to connect with friends, of course, but it's also proving to be a solid gaming experience in its own right, with a... | Read more »
You can now play game's on Facebook...
Facebook launched its new Instant Games platform in an exciting new attempt to engage its user base. As a result, you can now play a number of different games directly through Facebook Messenger. All of these games run with HTML5, meaning you play... | Read more »
Apollo Justice Ace Attorney (Games)
Apollo Justice Ace Attorney 1.00.00 Device: iOS Universal Category: Games Price: $.99, Version: 1.00.00 (iTunes) Description: Court Is Back In Session Star as rookie defense attorney, Apollo Justice, as he visits crime scenes,... | Read more »
KORG iWAVESTATION (Music)
KORG iWAVESTATION 1.0 Device: iOS Universal Category: Music Price: $19.99, Version: 1.0 (iTunes) Description: A revolutionary new world of sound.The Wave Sequence Synthesizer for iPad - KORG iWAVESTATION | Read more »
Don't Grind Guide: Tips for becomin...
Don’t Grind is a surprising, derpy little one touch game with fun hand-drawn graphics. The goal is simple -- get the high score without being chopped to bits. That can be tough when you’re not used to the game, and that’s compounded by the fact... | Read more »

Price Scanner via MacPrices.net

Parallels Toolbox 1.3 for Mac Offers 25 Singl...
Parallels has launched Parallels Toolbox 1.3 for Mac, an upgrade that adds five new utilities to the stand-alone application which was released in August and is available exclusively online at http... Read more
OWC Mercury Elite Pro Dual mini Ultra-Portabl...
OWC has introduced the new OWC Mercury Elite Pro Dual mini, a powerful yet ultra-portable dual-drive RAID solution. The new Mercury Elite Pro Dual mini packs phenomenal performance into a small... Read more
Clearance 13-inch Retina MacBook Pros availab...
B&H Photo has clearance 2015 13″ Retina Apple MacBook Pros available for up to $200 off original MSRP. Shipping is free, and B&H charges NY tax only: - 13″ 2.7GHz/128GB Retina MacBook Pro: $... Read more
Roundup of 2016 13-inch 2.0GHz MacBook Pro sa...
B&H has the non-Touch Bar 13″ MacBook Pros in stock today for $50-$100 off MSRP. Shipping is free, and B&H charges NY sales tax only: - 13″ 2.0GHz MacBook Pro Space Gray (MLL42LL/A): $1449 $... Read more
New 13-inch 2.0GHz Space Gray MacBook Pro in...
Adorama has the new 13″ 2.0GHz Space Gray MacBook Pro (non-Touch Bar, MLL42LL/A) in stock for $1499 including a free 3-year AppleCare Protection Plan. Shipping is free, and Adorama charges sales tax... Read more
Finnair Adopts iOS Enterprise iPad Apps from...
Finnair and IBM have announced a first-of-its-kind agreement to utilize iOS enterprise apps from IBM to support the airline’s overall digital transformation. Finnair is focused on Asia-Europe traffic... Read more
Tech21 Launches Evo Go iPhone 7 Case Availabl...
Tech21 has announced the launch of the Evo Go case for Apple iPhone 7 and iPhone 7 Plus, exclusively at T-Mobile. Available online and at participating T-Mobile stores nationwide, Evo Go cases start... Read more
Apple Turns (RED) with More Ways to Join the...
In recognition of World AIDS Day, Apple is offering more ways than ever for customers to join (RED) in its mission to create an AIDS-free generation. Apple is the worlds largest corporate contributor... Read more
Deals on new 15-inch Touch Bar MacBook Pros,...
B&H Photo has new 2016 Apple 15″ Touch Bar MacBook Pro models in stock today with some available for $50 off MSRP, each including free shipping plus NY sales tax only: - 15″ 2.7GHz Touch Bar... Read more
12-inch Retina MacBooks on sale for up to $10...
12-inch Retina MacBooks remain on sale at B&H Photo with models available for up to $100 off MSRP. Shipping is free, and B&H charges NY sales tax only. B&H will also include a free copy... Read more

Jobs Board

US- *Apple* Store Leader Program - Apple (Un...
…Summary Learn and grow as you explore the art of leadership at the Apple Store. You'll master our retail business inside and out through training, hands-on Read more
*Apple* Retail - Multiple Positions- White P...
Sales Specialist - Retail Customer Service and Sales Transform Apple Store visitors into loyal Apple customers. When customers enter the store, you're also the Read more
Automotive Detailer - *Apple* Used Autos -...
We are currently conductinginterviews and will be accepting applications for a part-time detailer. Apple Used Autos is a great place to work andstart a career. We Read more
*Apple* Retail - Multiple Positions - Apple,...
Job Description: Sales Specialist - Retail Customer Service and Sales Transform Apple Store visitors into loyal Apple customers. When customers enter the store, Read more
US- *Apple* Store Leader Program - Apple (Un...
…Summary Learn and grow as you explore the art of leadership at the Apple Store. You'll master our retail business inside and out through training, hands-on Read more
All contents are Copyright 1984-2011 by Xplain Corporation. All rights reserved. Theme designed by Icreon.