Windows Install

Pre-compiled PyMOL

Pre-compiled PyMOL is available free from Christoph Gohlke of the Laboratory for Fluorescence Dynamics, University of California, Irvine here.

For example install python 2.7 on windows, and then compile the open source pymol for free.

1. Install python, 2.7 for windows. Use the standard options.
2. Download [ http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol appropriate installer] and select according to your python version 2.7 and 32/64 bit system.
3. Run the downloaded installer
4. PyMOL is now installed in: C:\Python27\PyMOL
5. Run PyMOL by executing: C:\Python27\PyMOL\PyMOL.exe

You should make a shortcut to the PyMOL.exe tile and place in your Start menu.
If you right-click a .pdb file, and "Open with", and then point to C:\Python27\PyMOL\PyMOL.exe, you can double click .pdb files.

Extend PyMOL with additional scripts

If you now want to extend the capabilities of PyMOL, and take advantage of all the available plugins+scripts "out there", then do the following.

1. First install "numpy" as an available module to Python. [ http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy appropriate installer]
2. Download the script/plugin collection Pymol-script-repo from a .zip file from here
3. Unpack it to here: C:\Python27\PyMOL\Pymol-script-repo . Double check that the folder name is correct and the same.

Open "Notepad" and write:

Personal changes to opening of PyMOL

You can make a "pymolrc.pym" file, and put it under "C:\Users\YOU".
In the file you can write things that PyMOL should change from standard values, when it opens.
See more here.

Binary

To install PyMOL from the binaries, just run the executable you've downloaded.

Source

To get the latest features, you should download the PyMOL source from the project page.

Directions using CygWin

• Install CygWin. Make sure you install the following modules:

You should have similar packages installed as described here. Note, that you might need gcc-4.4 instead of gcc-4.5.

• • C++ (gcc or g++ package name)
  • Python
  • OpenGL
  • PNG
• run python setup.py install in the source directory
• run python setup2.py install in the source directory
• install Pmw

Problems & Solutions

Problem: Installing PyMol 0.98 on WinXP Pro SP2

If you get the following error while installing

 "16-bit Windows Subsystem.":
 "C:\WINDOWS\SYSTEM32\AUTOEXEC.NT. The system file is not
 suitable for running MS-DOS and Microsoft Windows applications.
 Choose 'Close' to terminate the application.

Fix: Sounds like the AUTOEXEC.NT file is corrupt. You can fix this problem by replacing

c:\WINDOWS\SYSTEM32\AUTOEXEC.NT

with the one in

c:\windows\repair

However if this doesn't work (or if the file is absent from this repair folder), use the file on the installation CDROM, it is

autoexec.nt_ 

in the i386 folder. Just type in a command window:

expand X:\i386\autoexec.nt_ c:\windows\system32\autoexec.nt

where X is the drive letter of your CDROM.

If this does not resolve your issue, visit this link: MS Support For This Issue where you may also find the answer to your question.

Problem: PyMol Binary Crashes

Video Driver

Fix: Try updating your video card's driver software. This is a common problem on laptops.

msvcr71.dll

Fix: find the file msvcr71.dll on your computer and copy it to the directory that PyMol was installed to.

Problem: Path Does Not Exist Error

Install Shield Problem with some Dell Laptops

With this problem irrespective of where you place the binaries for installing PyMol you receive an error claiming that the path\setup.exe does not exist.

Fix: Install the windows binary through 16-bit MS-DOS console.

First place the PyMol setup binaries in an easy to find folder, e.g. C:\PyMol

Use the RUN command via Windows Start.

In the CLI type COMMAND.COM (note CMD will not work as it is a native interface and not true DOS).

In the DOS CLI that opens go back to the root directory C:\ using the cd.. command.

Then go to the folder into which you placed PyMol, e.g. cd PyMol.

Then type in setup.exe.

PyMol should now install, simply type exit to close the DOS CLI

Using

Debugging

On Windows, you need to launch PyMOLWin.exe from a Windows command line with the "+2" option to prevent PyMOL from hiding the console window: (start menu -> run -> cmd [return])

cd c:\program files\delano scientific\pymol

pymolwin + 2