Free molecular software for mac

Science is SO IN. Be an uber-science-indie geek and make your desktop look hot AND impress your other geeky friends by pointing out the accuracy of these molecular structures!

All icons are aquafied and look best in 128x128 at 32bit mode.

Completly freeware for personal use.

PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. It can also perform many other valuable tasks (such as editing PDB files) to assist you in your research.
The extensible core PyMOL module (hosted here at SourceForge) is available free to everyone via the "Python" license (a simple BSD-like permission statement), but we ask all users to purchase a license and maintenance agreement in order to cover our development and support costs.

MoFa, the Molecular Fragment Miner, is a program that finds automatically molecular substructures and discriminative fragments in a set of molecule descriptions given some user defined parameters.

The very typical core structure of steroid molecules is a system of fused rings consisting of three 6-rings and one 5-ring. There may be different branches emerging from various ring atoms but all in all these ring structures are most characteristic.

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.

Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry.
Jmol was originally intended to be a fully functional replacement for XMol which was a molecular viewing program developed at the Minnesota Supercomputer Center.
Although the program executables were distributed, the source code was not available to users, and since the program has not been maintained, the free binary versions have become obsolete.
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.

The Amino Acid Table widget displays general information on amino acids (name, 3-letter code, 1-letter code, triplet and standard color code) conformed with the IUPAC-IUB recommendations.
Enhancements:
- New information on molecular weight, composition, polarity, hydrophobicity, pK and pI for amino acids.
This widget is free for all users. Download it now !

AlleleID 7.01 works great and has a friendly interface.

Major Features:

1. Designs real time PCR assays and microarrays for single templates, multiplex reactions and aligned sequences.
2. In-built ClustalW multiple sequence alignment capability.
3. Design support for TaqMan probes, TaqMan MGB probes, molecular beacons, FRET, SYBR Green and microarrays.
4. Ability to design minimal sets of oligos to differentiate strains from a mix.
5. Designs oligos that amplify and detect various species at one time by identifying the conserved regions.