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Installation

Windows

Recommendations

Minimal System Requirements

Unless you have prior experience with Python, we recommend installing a version of PyMOL which does not require an external Python interpreter. Avoid versions of which contain "-py21", "-py22", "-py23" or similar in the filename.

Python-Free Installation

  1. Download the ".zip" format archive. For example, 
    pymol-0_90-bin-win32.zip
  2. Extract the .zip file using WinZip (Windows XP can open .zip files directly).
  3. Double click on the "Setup" or "Setup.exe" icon in the folder.
  4. Answer the questions which follow.

You can now launch PyMOL from the Start menu.

Python-Dependent Installation

If you already have Python installed and wish to use PyMOL with that interpreter, the process is virtually identical. The only difference is that you need to download a version of PyMOL which matches your desired Python version in the filename. For example:

pymol-0_90-bin-win32-py22.zip
 would work with
Python-2.2.2.exe

 available from http://www.python.org .

MacOS X

Recommendations

Minimial Requirements

If you use Fink

PyMOL is part of the Fink ports collection.

sudo -s
apt-get pymol install
should be sufficient to get a functioning instance on your system. However, it may not be the most recent version. We also highly recommend installation of Apple's X Server, which enables PyMOL to access your accelerated graphics hardware.

If you do not use Fink

Option 1: MacPyMOL

At the request of various Macintosh users, as well as Apple itself, we have created MacPyMOL, a special native Aqua version of PyMOL for the Macintosh. The latest version of MacPyMOL can be downloaded from http://delsci.com/macpymol .

However, note that this version is an Incentive Product only available to PyMOL sponsors (but students and teachers are exempt from this requirement). For more information on MacPyMOL, contact support@delanoscientific.com.

Option 2: PyMOL X11 Hybrid

This version of PyMOL includes a native Aqua-based OpenGL window and an X11-based Tcl/Tk external GUI (graphical user interface). Before launching the PyMOL X11 Hybrid, you must have Apple's X11 server installed and launched. The advantage of using this version is that it is fully compatible with Open-Source PyMOL, and does not require Fink. However, unlike MacPyMOL, this version does not support direct export of QuickTime movies. This binary build is free, but not Open-Source.

  1. Download the "pymol-0_XX-bin-osx-x11-hybrid.dmg.gz" compressed disk image.
  2. Extract the archive and mount the disk image.
  3. Copy the "PyMOLX11Hybrid" folder to the main Applications folder on your hard disk.

You can then launch PyMOLX11Hybrid by double-clicking on the PyMOLX11Hybrid icon.

Linux and Unix

System Requirements

There are a several different ways to install PyMOL on Linux. Please consult the PyMOL Web Site for additional information.

Dependency-Free Approaches

These do not require installing any other packages in a privileged location on your system. All you need to do is download a "tar"-ball appropriate for your system, such as the following:

issue the following commands

gunzip < pymol-...-bin-...-.tgz | tar -xvf -
./setup.sh

which will install the program, and then

./pymol.com

will launch PyMOL. You may then want to make a symbol link for this file to ~/bin/pymol for easy launching.

ln -s $PWD/pymol.com ~/bin/pymol

Install a minimal dependency binary build.

Compile PyMOL from source along with the "ext" dependencies distribution.

Because the installation process is often subject to change, please see the INSTALL file from the current distribution for detailed instructions. In summary,

  1. Download, extract, configure, and compile the external dependencies.
  2. Download and extract the current PyMOL source distribution.
  3. Create a symbolic link from the external dependencies to "ext" in the PyMOL directory.
  4. Configure compilation by copying and modifying a "Rules.make" from the setup directory to reflect your system.
  5. Run "make" to build pymol.
  6. Create a pymol.com specific to your installation location.

You should be able to launch PyMOL by running pymol.com. I usually symbolic link this file into my "bin" directory as "pymol".

Dependency-Based Approaches

You must install the following packages on your system

   python (2.x), tcl (8.x), tk (8.x), libpng (1.x), zlib (1.x),
   glut (3.x), glut-devel (3.x), pmw*, and numeric* (numpy)
(* = not required for RPM packages.)

You then have several choices:

Using RedHat binary packages (RPMs).

rpm -i pymol-0.90-1.rh73.py22.i386.rpm

Using Python's distutils to compile and install PyMOL as a standard Python module.

python setup.py build      (as a user)
python setup.py install    (as root)
python setup2.py install   (as root)
You can now run PyMOL with "./pymol.com".

Using Makefiles with preinstalled system dependencies.

Because the installation process is often subject to change, please see the INSTALL file from the current distribution for detailed instructions. In summary,

  1. Download and extract the current PyMOL source distribution.
  2. Configure PyMOL by copying and modifying a "Rules.make" from the "setup" directory to reflect your system.
  3. Run "make" to build pymol.
  4. Create a pymol.com specific to your installation location.

You should be able to launch PyMOL by running pymol.com, and it may be convenient to add a symbolic link from this file into your "bin" directory as "pymol".

This chapter last updated June 2004 by Warren L. DeLano, Ph.D.

NOTE: This manual is a PyMOL Incentive Product with a One-Year Evaluation Period. You, your school, or your employer must purchase a PyMOL License & Maintenance Subscription to cover usage beyond the first year. We trust you to support the PyMOL project via the "honor" system, so please do your part! See Usage Terms for more information.
Copyright © 2004 DeLano Scientific LLC. All Rights Reserved.
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