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[[Category:Installation|Windows]]
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This page describes how to install PyMOL on Microsoft Windows.
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== Incentive PyMOL ==
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[http://www.schrodinger.com Schrödinger] provides an MSI installer to paying sponsors. The bundle also includes ready-to-use [[APBS]], [[morph|RigiMOL]], an MPEG encoder for movie export, and a small molecule energy minimization engine.
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Download: http://pymol.org/download
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== Open-Source PyMOL ==
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Open-Source PyMOL is available [https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/LICENSE free of charge]. It also allows sponsors to create highly customized PyMOL installations which might not be possible with the MSI installer.
  
== Installing ==
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Pre-compiled Open-Source PyMOL is available free from [http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol Christoph Gohlke of the Laboratory for Fluorescence Dynamics, University of California, Irvine].
== Pre-compiled PyMOL ==
 
Pre-compiled PyMOL is available free from Christoph Gohlke of the Laboratory for Fluorescence Dynamics, University of California, Irvine [http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol here].
 
  
 
# Install Python 2.7 for Windows (e.g., by going to http://www.python.org/downloads/). Use the standard options (which should mean that the installation directory is C:\Python27). It may be useful if C:\Python27 is listed in your system PATH variable.  
 
# Install Python 2.7 for Windows (e.g., by going to http://www.python.org/downloads/). Use the standard options (which should mean that the installation directory is C:\Python27). It may be useful if C:\Python27 is listed in your system PATH variable.  
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Now start pymol, and enjoy all the plugins available from the menu.
 
Now start pymol, and enjoy all the plugins available from the menu.
  
'''PyMoL''' shortcut<br>
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'''PyMOL''' shortcut<br>
 
Make a '''pymol''' directory in your homepath. '''mkdir %HOMEPATH%\pymol'''  Then make sure, PyMOL starts here, when you open the shortcut.<br>
 
Make a '''pymol''' directory in your homepath. '''mkdir %HOMEPATH%\pymol'''  Then make sure, PyMOL starts here, when you open the shortcut.<br>
Make a shotcut to the .cmd file, and modify it. <br>
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Make a shortcut to the .cmd file, and modify it. <br>
 
Target: C:\python27\PyMOL\pymol.cmd <br>
 
Target: C:\python27\PyMOL\pymol.cmd <br>
 
Start in: %HOMEPATH%\pymol
 
Start in: %HOMEPATH%\pymol
  
=== Personal changes to opening of PyMOL ===
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== See Also ==
You can make a "pymolrc.pym" file, and put it under "C:\Users\YOU". <br>
 
In the file you can write things that PyMOL should change from standard values, when it opens.<br>
 
See [[Pymolrc | more here.]]
 
 
 
== Binary ==
 
To install PyMOL from the binaries, just run the executable you've [http://pymol.sf.net/ downloaded].
 
 
 
== Source ==
 
To get the latest features, you should download the [http://sourceforge.net/svn/?group_id=4546 PyMOL source] from the [http://sourceforge.net/projects/pymol/ project page].
 
 
 
=== Directions using CygWin ===
 
* Install [http://www.cygwin.com/ CygWin].  Make sure you install the following modules:
 
You should have similar packages installed as described [http://www.pymolwiki.org/index.php/Linux_Install#Mint11_Linux_.28Ubuntu.29_-_Tested_for_PyMOL_1.4.1 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
 
 
 
  
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* [[pymolrc]]
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* [[Linux Install]]
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* [[MAC Install]]
  
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[[Category:Installation|Windows]]
 
[[Category:Technical Issues|Windows Install]]
 
[[Category:Technical Issues|Windows Install]]
 
[[Category:Windows]]
 
[[Category:Windows]]

Revision as of 17:21, 29 January 2016

This page describes how to install PyMOL on Microsoft Windows.

Incentive PyMOL

Schrödinger provides an MSI installer to paying sponsors. The bundle also includes ready-to-use APBS, RigiMOL, an MPEG encoder for movie export, and a small molecule energy minimization engine.

Download: http://pymol.org/download

Open-Source PyMOL

Open-Source PyMOL is available free of charge. It also allows sponsors to create highly customized PyMOL installations which might not be possible with the MSI installer.

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

  1. Install Python 2.7 for Windows (e.g., by going to http://www.python.org/downloads/). Use the standard options (which should mean that the installation directory is C:\Python27). It may be useful if C:\Python27 is listed in your system PATH variable.
  2. Download the appropriate wheel files, along with all requirement wheel files (including pip, Numpy and PMW) into a single file directory, e.g., C:\PyMOL_installation
  3. From this installation directory (to get there you can run
    cd C:\PyMOL_installation
    
    from the command prompt), run:
C:\Python27\python.exe pip-6.x.x-py2.py3-none-any.whl/pip install --no-index --find-links="%CD%" pymol_launcher

if C:\Python27 is part of your PATH variable, then running (where x refers to the version number of pip):

python pip-6.x.x-py2.py3-none-any.whl/pip install --no-index --find-links="%CD%" pymol_launcher

should suffice. To update PyMOL update the files in the PyMOL install directory and run:

pip install --upgrade --no-deps pymol.whl

where pymol.whl is replaced by the PyMOL wheel file name (not the launcher, the launcher should not require updating).

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. Select appropriate installer from here
  2. Download the script/plugin collection Pymol-script-repo from a .zip file from here
git clone https://github.com/Pymol-Scripts/Pymol-script-repo
  1. Unpack it to here: C:\Python27\Lib\site-packages\pymol\pymol_path\Pymol-script-repo Double check that the folder name is correct and the same.

Open "Notepad" and write.

# Add paths to sys.path so PyMOL can find modules and scripts
import sys, os
pymol_git = os.path.abspath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))
os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])

# Make setting changes to Plugin Manager
import pymol.plugins
pymol.plugins.preferences = {'instantsave': False, 'verbose': False}
pymol.plugins.autoload = {'apbs_tools': False}
pymol.plugins.set_startup_path([os.path.join(pymol_git, 'plugins'), os.path.join(sys.prefix, 'Lib', 'site-packages', 'pmg_tk', 'startup')])
pymol.plugins.preferences = {'instantsave': True, 'verbose': False}

Then "File->Save as->All files-> C:\Python27\Lib\site-packages\pymol\pymol_path\run_on_startup.py

Now start pymol, and enjoy all the plugins available from the menu.

PyMOL shortcut
Make a pymol directory in your homepath. mkdir %HOMEPATH%\pymol Then make sure, PyMOL starts here, when you open the shortcut.
Make a shortcut to the .cmd file, and modify it.
Target: C:\python27\PyMOL\pymol.cmd
Start in: %HOMEPATH%\pymol

See Also