Troubleshooting – Installation Problems

If you have previous version of PyRx installed and are having problems installing the new version, please remove C:\Program Files\PyRx folder using Unlocker, for instance, prior to installing this new version.

To start the installer grant execute permission and run it as follows:

chmod +x PyRx-*-linux-x86_64-install
./PyRx-*-linux-x86_64-install

Troubleshooting – Startup Problems

Please run the following command if PyRx fails to start:

• Fedora: sudo yum install -y libpng12.x86_64 SDL.x86_64 mesa-libGLU.x86_64
• Ubuntu (following Fix libpng12-0 Missing In Ubuntu 18.04, 19.10, 20.04 Or 20.10):sudo add-apt-repository ppa:linuxuprising/libpng12

  sudo apt update
  sudo apt-get install libpng12-0 libglu1-mesa libsdl1.2debian

• SUSE: sudo zypper install libpng12-0 Mesa-libGLU1 SDL

Notes on the free version. 0.8 version is 32-bit. To run 64-bit version on Linux download pyrx-0.9.2-linux-x86_64.tar.gz and run the following commands to get started:

tar -xzvf pyrx-0.9.2-linux-x86_64.tar.gz 
cd PyRx
./run.sh 

Please note that current version of PyRx does not work with the latest version of macOS, since starting with macOS Catalina, 32-bit apps are no longer compatible with macOS.

To install PyRx open PyRx-x.y.z.dmg in Finder, Control-click or right click on PyRx-x.y.z and select Open. Once PyRx is successfully installed, PyRx.app will be available under Applications folder.

Instructions for Installing PyRx from Source

PyRx depends on many packages that might not be easy to install.

Please try binary installer corresponding to your OS first (see above).

If that fails, you’ll need to install the following list of packages that PyRx depends on.

Please note that installing PyRx from source is challenging and requires expert Python programming experience.

• Python – a programming/scripting language – python.org.

• AutoDockTools, used to generate input files – mgltools.scripps.edu.

• wxPython for cross-platform GUI – wxpython.org.

• The Visualization ToolKit (VTK) for 3D computer graphics – vtk.org by Kitware, Inc.

• Enthought Tool Suite, including Traits, for application building blocks – code.enthought.com.

• Opal Toolkit for running AutoDock remotely using Web services – opal.nbcr.net.

  You’ll need to install Python Opal Web Service Client. PyRx is set to use ws.nbcr.net servicer by default.
  If you are planning to create your own grid/cloud, you’ll need to install Opal Server as well.

• Open Babel for importing SDF files, removing salts and energy minimization – openbabel.org.

• AutoDock, used as a docking software – http://autodock.scripps.edu (optional).

  Only remote execution mode is enabled if PyRx can’t find autodock binaries.

• ePMV, embedded Python Molecular Viewer – epmv.scripps.edu.

Congradulations if you managed to install all the dependencies and read this far.

You are now only a few clicks away from using PyRx. Download and uppack PyRx-0.9-Source.zip (760 KB). The latest version of PyRx source code is also available at https://sourceforge.net/projects/pyrx/develop Now, do standard python install:

python setup.py install

Starting PyRx on Different Platforms

Windows Users – double click on runPyRx.py or run python runPyRx.py from command line.

Linux Users – add MGLTools to your PYTHONPATH:

csh - setenv PYTHONPATH/usr/local/MGLTools-$Version/MGLToolsPckgs:/usr/local/MGLTools-$Version/lib/python2.6/site-packages
bash - PYTHONPATH="/usr/local/MGLTools-$Version/MGLToolsPckgs:/usr/local/MGLTools-$Version/lib/python2.6/site-packages"

Run “python runPyRx.py” from command line.

Mac OS X Users – add MGLTools to your PYTHONPATH:

export PYTHONPATH="/Library/MGLTools/$Version/MGLToolsPckgs/:/Library/MGLTools/$Version/lib/python2.6/site-packages"

Run pythonw runPyRx.py from command line.