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• PyMOL is a powerful utility for studying proteins, DNA, and other biological molecules. This allows you to download the software for your Mac or PC system. Installation is straightforward, and PyMOL can be installed like any other PC or Macintosh software. During the installation process on a PC, you may be presented with several dialogs.
• The revisions made here are in an attempt to adapt this plugin, which works well with Python 2.7.9 and PrMOL 1.7.x on Linux or Mac for use on Windows. As of 28 March 2015, this version now appears to work reasonably well under both OS X and Windows XP.

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This FAQ applies to: AutoDock 4

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You should have downloaded a file with a name such as 'autodocksuite-4.2.1-i86Linux2.tar.gz' for Linux, and 'autodocksuite-4.2.1-i86Darwin8' or 'autodocksuite-4.2.1-ppcDarwin8' for Mac OS X.

Download the installer to your hard disk and double-click to launch. Answer questions asked or click “Next” as appropriate to complete the installation. Launch the program by selecting “PyMOL” from “All Programs” in the “Start” menu.

At the command line, change directory to the directory where you downloaded the file, <download-directory> (Note: you should substitute <download-directory> with the full path to where the downloaded file is):

Now let's extract the contents from the GNU-zipped tar file; in this example, we assume you have downloaded the Linux binaries:

This will create a new directory called 'i86Linux2'. In it, you will find two executables, called 'autodock4' and 'autogrid4'. Let's change directory there first:

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Now move the executables to the directory where you normally keep your binaries. On Linux and Mac OS X, this is often /usr/local/bin. The main thing is that this directory is in your path.

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Note: you have to have administrative privileges to do it (either switching user to root or by using sudo).
As root: As regular user (you have to type your user password): Now every time you open a new shell or Terminal, you should now be able to run AutoGrid 4 and AutoDock 4.

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