MAC Install

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Installing MacPyMOL

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Essentials

The download is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, scrollbutton mouse that works well with pymol and permits horizontal scrolling. Most other mice will also work well.

One word of warning: Do not install 3rd party drivers for multi-button mice if you can avoid it. These often mess with the mapping of the middle button or have other horrific side effects. Fortunately, with OS X, you should not need to.

I (Bill Scott) wrote a pymol shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable that lives in MacPyMOL.app/Contents/MacOS/PyMOL and pass arguments to it.

Extras

You don't need any of these to use MacPyMOL. But you didn't really need a Mac either. Face it: You need these.

Mighty Mouse

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A 3-button mouse is essential. Apple's Mighty Mouse is an extra treat.

PowerMate Dial

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The PowerMate dial works nicely with pymol.

Stereo

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The latest Macs finally support stereo in a window. There is more information in the Monitors Hardware Options section.

Installing X-windows based pymol on Mac OS X

Why would you want to do this?

1. You want to run a free, guilt-free, open-source version of pymol
2. You just happen to prefer the tkinter menu
3. You want to use plugins, for example, the apbs plugin for free grasp-like electrostatic calculations.

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Simplest Installation

Install pymol with Fink

http://pdb.finkproject.org/img/mlogo.png

By far the simplest way to install the X-windows based version of pymol on OS X is by using the fink package management system. To compile it, all you need to do is issue the command

fink install pymol-py24

(This will install python2.4 in fink, along with an X-windows based tkinter. There are also versions that permit you to install pymol to interact with python2.3 and even python2.2. Fink uses its own unix-type python installation, but you can trick pymol into using the aqua framework to get a prettier GUI after the fact.)

The fink pymol package currently exists in the unstable branch of fink, so you will either have to activate the unstable branch or make the following symbolic links:

sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.

You might need to create the latter directory if it doesn't already exist, i.e., issue the command

sudo mkdir -p /sw/fink/dists/local/main/finkinfo

I (wgscott) have put a whole lot of further information on how to use fink to install crystallographic software on my own wiki and website, including instructions on how to install precompiled binary packages using fink.

The fink pymol package is currently maintained by Jack Howarth.

Install APBS and friends with fink

To use the electrostatics plugin, you will need APBS and its dependencies. These are also available as fink packages, and include apbs, maloc and pdb2pqr. If you have multiple processors available, you might wish to install the mpi version of apbs.

Issuing the command

fink install apbs

will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin.

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