From OS X Scientific Computing

Quick link to Scientific Computing on Ubuntu for our Linux friends.

---

Basic Aspects of Scientific Computing on OS X

This wiki evolved from my Crystallography on OS X website, but it is designed to treat a few topics in more depth, thus augmenting that website. I would also like to make this a little more general, to cover topics such as NFS networks, that are of interest to a wider audience. More specifically, this wiki is intended to provide more detailed instructions for specialized topics, such as getting your fink installation to use packages that I have pre-compiled. Up until now, I've been putting these sorts of details on the main web site, but frequently there is outdated information, simply because I can't keep track of it all. In addition, there is no reason why the user community should not be able to edit and add to this stuff. It is after all intended to be a community resource. If you see something that is out of date, or find a broken link, or think there is an omission, please feel free to fix it. Please don't delete my hard work.

How to Participate

If you are not a spammer, I would value your participation. I am afraid however that I must request that you email me so I can create an account for you. Please send me your preferred username (and convince me you are not a spammer if you don't know me). Sorry to do this. I am completely open to less drastic approaches. wgscott AT users Dot sourceforge dOt net

Table of Contents for this wiki

• Index of Pages

1. For the Absolute Beginner
2. Quick Start
   1. Install Apple's Xcode
   2. Install Apple's X11.app
   3. Install Fink (and MacPorts if you need it)
   4. Getting your fink installation to use packages that I have pre-compiled
3. General Topics
   1. Augmenting the OS X Unix Environment, Part I: The Xcode Developer Tools
   2. Augmenting the OS X Unix Environment, Part II: An X11 windowing system
   3. Augmenting the OS X Unix Environment, Part III: The Fink Package Management System
   4. Unix and OS X: The Absolute Essentials
   5. Unix and OS X: Terminal, iTerm and other alternatives
   6. Unix and OS X: Third-Party Unix Software
   7. Fortran alternatives for intel macs
   8. Editors for OS X
   9. Extras I Can't Live Without
   10. ZSH on OS X
   11. Networking
       1. SSH and Tunneling
       2. NFS
       3. Running a Mail Server
4. Crystallography on OS X
   1. Crystallography Programs
      1. My Crystallography on OS X website
      2. Installing CCP4 on OS X
      3. Installing Coot on OS X
      4. Installing CNS on OS X
      5. Installing Phenix and CCTBX on OS X
      6. Installing Shelx on OS X
      7. Installing Sharp on OS X
      8. Installing EDEN on OS X
      9. Installing Solve on OS X
      10. Installing O on OS X
      11. Installing PyMol on OS X
      12. Installing USF programs automatically on OS X
   2. Using Fink to install pre-compiled crystallography software very quickly
      1. getting your fink installation to use packages that I have pre-compiled
         1. Manually install one or two packages
            1. Manually install coot binary
            2. Manually install CCP4 fink debian packages
            3. Manually install a binary CNS package
   3. Molecular Visualization
      1. Molecular Graphics Display Programs on OS X
         1. O
         2. MacPyMol
         3. Coot
         4. others
5. Biophysics on OS X
6. NMR on OS X
7. Chemistry on OS X

Off-Topic Subjects

1. Specific Programs
   1. Coot wiki
   2. Eden
   3. PyMol
2. Scientific Computing on Ubuntu Linux (It's not Mac OS X. Sue me.)
3. Running Linux via Parallels inside another operating system Run linux without every leaving OS X or Windoze.
4. Sandbox Experiment here.