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Instructions for Installing MGLTools on Linux

by Sargis Dallakyan last modified 2012-02-02 14:32
This page provides step-by-step instructions for installing MGLTools on Linux using a standalone installer.
1) Download the installer, grant execute permission and run the installer.
To grant execute permission, type the following command at a command prompt:
chmod +x MGLTools-$Version-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-$Version for the root user and $HOME/MGLTools-$Version 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.

See also: Step by step installation of MGLTools on Ubuntu Linux 8.04.

Setting up Your Environment for Command Line Usage

  To be able to start any of these applications in a Terminal Window
  you will need to:
  - either add "/usr/local/MGLTools-1.5.6/share/bin" to the path environment
    variable in your .cshrc or .bashrc as in the following example:
     .cshrc  - set path = (/usr/local/MGLTools-1.5.6/bin $path)
     .bashrc - export PATH="/usr/local/MGLTools-1.5.6/bin:"$PATH
  - or create aliases in your .cshrc or .bashrc as in the next examples:
     .cshrc:
     alias pmv /usr/local/MGLTools-1.5.6/bin/pmv
     alias adt /usr/local/MGLTools-1.5.6/bin/adt
     alias vision /usr/local/MGLTools-1.5.6/bin/vision
     alias pythonsh /usr/local/MGLTools-1.5.6/bin/pythonsh
     .bashrc:
     alias pmv='/usr/local/MGLTools-1.5.6/bin/pmv'
     alias adt='/usr/local/MGLTools-1.5.6/bin/adt'
     alias vision='/usr/local/MGLTools-1.5.6/bin/vision'
     alias pythonsh='/usr/local/MGLTools-1.5.6/bin/pythonsh'

Rehash your path, if needed, for these changes to be in effect:
       c-shell:
        > rehash
       bash-shell:
        > hash

To use PMV, ADT or VISION type pmv, adt or vision respectively;
for example:
     > pmv

A Python Molecule Viewer should come up.  You can load files from the
/usr/local/MGLTools-1.5.6/Data directory and start playing with PMV. 
Simple networks and data for VISION are located in
/usr/local/MGLTools-1.5.6/MGLToolsPckgs/Vision/Examples.

To run Python interpreter type "pythonsh":
    > pythonsh                   
               
**************************************************************************
**  Pmv script command line options
**************************************************************************

"pmv" script can be used with the following options:

        -h or --help       : print help message
        -a or --again      : play back lastlog file
        --overwriteLog     : overwrite log file
        --uniqueLog        : create a log file with a unique name
        --noLog            : turn off logging
        --die              : do not start GUI event loop
        --customizer file  : run the user specified file
        --lib packageName  : add a libraries of commands
    -d or --dmode modes : specify a display mode
            modes can be any a combination of display mode
           'cpk'  : cpk
           'lines': lines
           'ss'   : secondary structure ribbon
           'sb'   : sticks and balls
           'ms'   : molecular surface
           'ca'   : C-alpha trace
           'bt'   : backbone trace
           'sp'   : CA-spline
           'sssb' : secondary structure for proteins,
                    sticks and balls for other residues with bonds
                lines for other residues without bonds

    -c or --cmode modes : specify a dispaly mode
                color scheme:
            'ca' : color by atom
            'cr' : color by residue (RASMOL scheme)
            'cc' : color by chain
            'cm' : color by molecule
            'cdg': color using David Goodsell's scheme
            'cs' : color residues using Shapely scheme
            'css': color by secondary structure element
    '-i', '--interactive' : PMV interactive shell

    --opt            : run Python in optimized mode

 EXAMPLE::
     Display protein as ribbon, non protein as sticks and balls
     and color by atom type
             pmv -i --dmode sssb --cmode cr myprot.pdb
             pmv -i -m sssb -c cr myprot.pdb

Troubleshooting

Problems with standalone installer?
Download tar.gz instead 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.
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-1.5.6/bin/python. If the missing library is libstdc++.so.5, 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: http://mgltools.scripps.edu/documentation/how-to/hardware-opengl. 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 http://www.pythonware.com/products/pil/, unpack and cd to Imaging folder. Then use python shipped with mgltools to install it:
path-to-mgltools/bin/python setup.py install
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 http://www.cgl.ucsf.edu/chimera/graphics/graphicsbugs.html
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: http://www.cgl.ucsf.edu/chimera/graphics/graphicsbugs.html. 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 http://ati.amd.com/support/driver.html
For all other issues, please Contact Us with detailed information on how to reproduce the bug.

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