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Instructions for Installing MGLTools on Linux

by Sargis Dallakyan last modified 2011-05-18 10:02

This page provides step-by-step instructions for installing MGLTools on Linux using a standalone installer.

1) Download MGLTools-1.5.4-Linux-x86-Install grant execute permission and run the installer.
To grant execute permission, type the following command at a command prompt:
chmod +x MGLTools-1.5.4-Linux-x86-Install

You can also use file manager to grant execute permission (right-click on the downloaded file and select Properties).
See Troubleshooting if installer fails to start.
2) In the install wizard, click Next, select the destination and click Next again.

The default destination is /usr/local/MGLTools-1.5.4 for the root user and $HOME/MGLTools-1.5.4 for all others. Please wait a few moments until the "License Agreements for add-on packages" window appears.

3) Complete the "License Agreements for add-on packages" form.

See Filling add-on packages license form for details.

4) Finally, click Finish to complete installation

The README file contains detailed information on how to setup your environmental variables for command line usage.

Ubuntu/Debian users can use apt-get install autodocktools to install autodocktools, for instance. Read MGLTools is Available for Debian for more info. See also: Step by step installation of MGLTools on Ubuntu Linux 8.04.

Launching ADT, PMV or Vision

Click any of the following Desktop Shortcuts created by installer:

ADT 1.5.4

PMV 1.5.4

Vision 1.5.4

You can also run corresponding scripts located in <%InstallDir%>/bin, where <%InstallDir%> is the installation folder chosen in step 2. Run these scripts with the -h or --help option to print a usage guide. Our installer adds <%InstallDir%>/bin to your path, so you don't have to type the full path. The installer also creates the following Program Folder Shortcuts: for your convenience: menu.png

MGLTools Version
AutoDockTools Version
PMV Version
Vision Version
Update Manager Version
Uninstall Version

Note: our installers replace first line of ADT scripts located in <%InstallDir%>/MGLToolsPckgs/AutoDockTools/Utilities24 from #!/usr/bin/env python to #!/usr/bin/env <%InstallDir%>/bin/pythonsh.


Problems with standalone installer?
Download mgltools_i86Linux2_1.5.4.tar.gz and follow instructions in the README included in the tarball. These are binary tarballs that contain a pre-compiled Python interpreter and various platform dependent packages included in the binary distribution of MGLTools. On 64-bit Linux, for instance, our installer requires 32-bit X11 libraries. You can either install 32-bit X11 or install MGLTools from the tarball.
You are getting "ERROR Installing MGLTools binaries!!!".
This happens when there are missing libraries. Since we include all non standard libraries in our binary distribution, this probably means that there is a version mismatch in one of the core linux libraries. See, for instance, Yet another Unix nightmare: statically linking libstdc++.
To find out what library is missing run MGLTools-1.5.4/bin/python. If the missing library is, installing compat-libstdc++ should fix the problem. Ubuntu 8 users: use Synaptic Package Manager, search for libstdc++5 and install libstdc++5 package.
TclError: Togl: couldn't get visual.
Please install graphics driver from your graphics card manufacturer: See also ADL: ... Togl: couldn't get visual RESOLVED.
ImportError: The _imaging C module is not installed
Download PIL 1.1.6 Source Kit from, unpack and cd to Imaging folder. Then use python shipped with MGLTools to install it:
path-to-mgltools/bin/python install
Commercial Support for PIL is available through PythonWare.
intel.prim.flush failed on Intel graphics card.
Please install libdrm-dev if you are using Xorg. XFree86 users please try Intel Graphics Driver. See also
Problems with Platform Dependent packages?
32-bit platform-dependent packages are built on RHEL 4 with gcc version 3.2.3 and swig version 1.3.31 (GLIBC_2.3, libstdc++.5.X). If you are running a different distribution of Linux and having problems using MGLTools, please download source tarball and follow instructions in the included README.
Shortcuts are not visible.
You might need to logout and login again to see changes after (un)inistall. These shortcuts are installed in ~/Dersktop, ~/.local/applications, ~/.local/share/desktop-directories and ~/.config/menus/applications-merged.
Bugs in graphics drivers?
Please see: Many graphics driver bugs observed in MGLTools have similar solutions

Known Issues

X server crashes on machines with ATI graphics card.
Please install the latest drivers from
For all other issues, please Contact Us with detailed information on how to reproduce the bug.

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