Free molecules software for mac

Beware of Molecules is a molecular weight calculator for the rest of us.
NOTE: Users of 3.3.4 make sure to read the included Migration Info.
Enhancements:
- Totally rebuilt, ground up
- Internet database update
- New and improved smaller file size.

COLUMBUS is 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.
An important feature of COLUMBUS is its flexibility. In addition to standard classes of reference wave functions, such as CAS or RAS, calculations can be performed with selected reference configurations. Though the multi-reference aspect of COLUMBUS is emphasized, single-reference calculations can also be carried out very efficiently.
Main features:
- SCF - closed-shell and restricted open-shell
- MCSCF - general MCSCF with quadratic convergence including state-averaging
- MR-CISD - direct CI for all single and double excitations from an arbitrary set of reference configurations
- MR-ACPF and MR-AQCC - modified MRCISD methods that include iterative size-extensivity corrections
- Analytic gradient for MCSCF, MR-CISD, MR-ACPF and MR-AQCC
- Analytic MR-CISD nonadiabatic coupling vector
- Automatic geometry optimization and saddle-point searches
- Automatic searches for minima on the crossing seam (conical intersections)
- Spin/orbit CI
- A massively-parallel version of the MR-CISD, MR-AQCC and respective two-electron density program sections.
Enhancements:
- Analytic MR-CISD/AQCC gradient for excited states based on state-averaged MCSCF calculations
- Analytic MR-CISD nonadiabatic coupling vector
- Automatic searches for minima and saddle points in excited states
- Automatic searches for minima on the crossing seam (conical intersections)
- Integration of the GUGA spin-orbit CI program (still in test phase)
- A massively parallel CI and two-electron density code
- Enhanced user interface including visualization features via MOLDEN.

MolView X is the OSX version of MolView. Nearly all of the features of MolView have been ported. MolViewX now outputs POV-Ray files for rendering. MolViewX also outputs VRML files for Strata 3DPro and a number of UNIX based applications.

MolViewX can read several types of coordinate files and display ribbon, CPK, stick, ball&stick, and surface figures. The interface is completely interactive (i.e. no comand line input). There are countless options that control the display colors and characteristics.

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. In addition, the user can open 2 different structures and even perform 3D alignments on them.

Also, subsets of the structure can be stored as MOL files and be read in later.

Bioclipse, as any RCP application, is based on a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as software updates, preferences, help system, cross-platform deployment etc.
Bioclipse will provide functionality for chemo and bioinformatics, and extension points that easily can be extended by plugins to provide added functionality. The first version of Bioclipse includes a CDK-plugin (bc_cdk) to provide a chemoinformatic backend, a Jmol-plugin (bc_jmol) for 3D-visualization and a general logging plugin.
NOTE: Bioclipse is licensed and distributed under the terms of the Eclipse Public License.

Main features:
- Import and export in various file formats
- Visual editing of molecular 2D-structures
- 3D-visualization of molecules and proteins
- Editing and visualization of sequences and features (DNA, RNA, proteins etc)
- Graphing and editing of various types of spectra, e. g. NMR, MS
- Retrieval of resources (sequences, proteins, etc) from public data repositories
- Scripting of 3D-visualizations with syntax highlighting and content assistance
- PDB-editor with syntax highlighting for working with PDB files
- CMLRSS-viewer for downloading chemical content published on the web using RSS-feeds
- Chemtree for displaying a hierarchical view of molecular and macromolecular substructures
- Visualization of syandard chemical properties
- Powerful scripting language based on Mozilla Rhino for automating tasks
- Integrated, searchable help-system
- Connection with external programs, e. g. PyMol

MacVector 11.0.3 offers you the ability of use program available for sequence analysis.

Major Features:

1. Graphical Sequence Editing: MacVector can read and write DNA and Protein sequences in most popular file formats. In addition to directly editing sequences and features/annotations, MacVector has an intuitive "Click Cloning" graphical interface that lets you easily replicate laboratory cloning experiments to create new molecules.
   
2. Gateway and Topo Cloning: MacVector supports the populay Gateway, TOPO TA and Zero Blunt cloning technologies from Invitrogen. With a few simple clicks from an intuitive graphical interface, you can replicate your biological manipulations at the bench to create new molecules with the correct sequences across the cloning and recombination junctions.
3. Auto Annotation: You can scan an unannotated or partially annotated sequence against a folder on your hard drive and MacVector will identify matching features in sequences in the target folder and add them to your sequence.
   
4. Primer Design: You can design primers for either PCR or Sequencing/Hybridization probes use in experiments.
5. DNA Analysis: MacVector provides a wide variety of using "Dot-Plot" analysis and scanned for Proteolytic cleavage sites and amino acid sequence motifs. A comprehensive Protein Analysis Toolbox provides a wide variety of algorithms for analyzing the composition of proteins and presenting the results in graphical and tabular formats.
6. Database Searching: MacVector has built-in Internet connectivity to the NCBI BLAST and Entrez databases. You can directly search Entrez for DNA or Protein sequences based on features, authors, keywords etc and directly download them into MacVector, complete with all features and annotations. The built-in BLAST interface lets you submit multiple BLAST jobs using a FastA algorithm, allowing for "local" database searches.
7. Multiple Sequence Alignment: You can align unlimited numbers of DNA or Protein sequences ustalW algorithm built in to MacVector. A full-featured editor lets you make manual adjusing a wide variety of cused for two different functions, Sequence Confirmation and cDNA Alignment. This is included with MacVector and allows you to import trace files or sequence files and assemble them against a template sequence. This is ideal for small scale sequencing projects, especially resequencing.
   

Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Mac OS X, Windows, and Linux/Unix systems.
The JmolApplet is a web browser applet that may be integrated into web pages.
The Jmol application is a standalone Java application that runs on the desktop.
The JmolViewer is a development tool kit that can be integrated into other Java applications.

Main features:
- True 3D graphics engine that requires no special hardware.
- 24 bit color with accurate lighting and shading.
- Substantially higher rendering performance.
- Handles large macromolecules with excellent performance.
- Protein/nucleic acid secondary structure graphics.
- RasMol/Chime script compatibility.

Enhancements
- bug fix: Application setAppletContext null pointer
- bug fix: point + integer wrong result
- bug fix: biomolecules for new PDB format
- bug fix: isosurface cavity colorscheme not applied
- bug fix: isosurface cavity colorscheme "sets" error
- bug fix: selected connected(hbond) not working.

EasyChem is designed to draw chemical molecules in an intuitive way, with a very high quality (designed for book-publishing). Exporting is done to various formats (PostScript, Fig, LaTeX, etc.) to help you integrate your drawing in any software you use.

Ive been using some Linux tools to draw chemical structures (chemtool, xdrawchem, etc.) for some time, but was never satisfied of the result. Then, I wrote part of a book about chemistry (exam solutions, published and sold in France).

The only tool able to draw press-quality molecules was... xfig, with a good library! To solve this problem (since I will write again next year), I decided to develop my own software: EasyChem.