Biophysics on OS X

From OS X Scientific Computing

Contents 1 Preliminaries 2 Crystallography Programs 3 Molecular Display Programs 4 Electrostatics Calculations 4.1 APBS 4.2 Other Options 5 Ab initio Quantum Calculations 6 Molecular Modeling Programs 7 Bio-informatics Programs 8 NMR Programs 9 Other Scientific Programs you can Install via Fink

Preliminaries

• Setting up Unix GNU Freeware and OpenSource programs on OS X

• Scientific Computing on OS X

Crystallography Programs

• Crystallography on OS X website

• Resources on this Wiki

Molecular Display Programs

• Coot on OS X

• PyMol on Mac OS X

• O

• Link to my annotated web page

Electrostatics Calculations

There are a few free alternatives to commercial software that work on OS X.

APBS

The Adaptive Poisson-Boltzmann Solver is software for evaluating the electrostatic properties of nanoscale biomolecular systems written by Nathan Baker.

By far the easiest way to get this is to install the abps fink package, and run it from within the fink pymol package. I've described how to do so on the APBS page of the PyMOL wiki.

Briefly, you should do the following:

1. First, register your use of the software. This will keep everyone happy.
2. Second, if you don't already have the fink package management system, now is a good time to get it. Here is a quick-start set of instructions for getting X-windows, compilers, and fink all installed.
3. Once you are up and going, activate the unstable branch in fink, and then issue the commands

fink self-update
fink install apbs

or if you want to use the multi-processor version, issue

fink self-update
fink install apbs

Then install the X-windows based version of pymol using the command

fink install pymol-py25

Note that the fink version of pymol already has the latest version of the APBS plugin. You are set to go!

Further details, as well as screen shots, are given elsewhere in this wiki.

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Other Options

There is a fink package for mead but compiling it has been problematic on intel. I also find it impossible to run.

Ab initio Quantum Calculations

GAMESS is a general ab initio quantum chemistry package that will run on OS X.

Molecular Modeling Programs

• COOT lets you build proteins and nucleic acids

• Tinker is a complete and general package for molecular mechanics and dynamics

• Namot is a buggy program to build nucleic acids. Use coot if you can.

• RNAmotif can be used to build RNA models.

• NAB Nucleic Acid Builder is another option.

• MMTK Molecular Modeling ToolKit is python-based.

Bio-informatics Programs

Here is a partial and somewhat outdated list of bioinformatics packages in fink

NMR Programs

NMR on OS X

Other Scientific Programs you can Install via Fink

A listing of science packages in fink that is up to date.