FAQs

PMV is the Python Molecule Viewer, which allows one to view molecules and rotate them in 3D. Molecules can be colored and rendered in various ways, including as secondary structure ribbons or as molecular surfaces.  PMV has a sophisticated selection mechanism based on its four level hierarchical data structure: Molecules are at the top and contain Chains, which contain Residues, which consist of Atoms. PMV is written in Python, an interpreted, object-oriented language that is easy to learn.  While the the user accesses PMV commands via the menus of its Graphical User Interface, PMV records these operations in a file called 'mvAll.log.py'.  This log file is a pure Python script which can be edited and/or sourced at a later time, to re-do these earlier operations.  PMV also offers an extremely useful 'Undo' command for most operations.

ADT, also known as AutoDockTools, consists of 5 specialized modules for PMV, so learning about PMV helps to understand what is possible with ADT.  Take a look at both the ADT Tutorial and PMV Tutorial.  ADT is an easy-to-use graphical front-end to the automated docking software packages AutoDock and AutoGrid. ADT provides menus to:

• set up a ligand (the 'moving' molecule to be docked) and write out a PDBQ file;
• set up a macromolecule (the 'fixed' molecule being docked to) and output a PDBQS file with solvation parameters;
• assign Kollman United Atom charged to a protein or peptide, or DNA or RNA;
• compute Gasteiger PEOE partial charges for small molecules or cofactors;
• add polar hydrogens, or 'merge' non-polar hydrogens;
  
• set up a grid box for atomic affinity grid maps and electrostatic potential maps around the target macromolecule; 
• set various docking parameters; 
• write GPF and DPF files (grid parameter and docking parameter files); 
• launch AutoDock and AutoGrid calculations;
• read in DLG files (docking log files) and visualize AutoDock results; 
• visualize grid maps by isocontouring them in 3D(using isocountouring library developed in Chandrajit Bajaj's group at UT Austin - part of UTpackages - http://ccvweb.csres.utexas.edu/software ); and also 
• cluster and re-cluster docking results in various ways.
  

VISION, or the Visual Programming Environment, is an advanced environment in which Python-based object-oriented components can be dragged-and-dropped and 'wired' together to create new applications. It consists of various libraries of 'nodes', each node performing some well-defined computational task. Molecules can be read in, for example, using one of the 'MolKit' library's nodes.

The following is a list of Python packages included with MGLTools:

Binaries of platform dependent packages are included in the installers for all supported platforms. Linux and Mac installers also include a pre-compiled Python interpreter. Windows installer downloads and installs Python, if necessary.

Please note that AutoDock and AutoGrid are not included - they are distributed via a separate mechanism. Please visit autodock.scripps.edu for details.

MGLToolsPckgs is a folder used to store  MGLTools packages. It is located in MGLTools installation folder (<%InstallDir%>) that  depends on the platform and on the version of MGLTools. The following are default locations for <%InstallDir%>:

Linux

/usr/local/MGLTools-1.5.0 if you install as root or $HOME/MGLTools-1.5.0 if you install as a regular user.

Mac OS X

/Library/MGLTools/1.5.0

Windows

C:\Program Files\MGLTools 1.5.0

If you installed MGLTools from source, MGLToolsPckgs is located in site-packages folder of your Python installation.  See the README file provided in the source tarball for more details.

There is a bug in freeglut-2.4.0-4 that causes this problem. Please replace freeglut with version 2.2.0-1. The following commands should do this.

1. Go to Control Panel -> System-> Advanced.
2. Click 'Environment Variables' button.
3. In the 'System Variables' panel that appears, click New and enter PYTHONPATH in the 'Variable Name' field. In the 'Variable Value' field enter path to MGLToolsPckgs (e.g. C:\Program Files\MGLTools-1.4.5\MGLToolsPckgs).
   

Note that our standalone installer creates/modifies C:\Python24\Lib\sitecustomize.py to include the latest version of MGLToolsPckgs in your path.

This ImportError means that Python interpreter can't find appropriate packages from MGLTools. Please run these scripts using pythonsh (e.g. pythonsh prepare_ligand.py) located in:

Linux $MGL_ROOT/bin, where $MGL_ROOT is either /usr/local/MGLTools-1.5.2 or $HOME/MGLTools-1.5.2

Mac OS X /Library/MGLTools/1.5.2/bin

Windows users: our installer creates/modifies C:\Python25\Lib\sitecustomize.py and you should be able to run prepare_ligand.py as follows:

C:\Python25\python.exe prepare_ligand.py

Python Path

pythonsh is a shell script that sets appropriate environment variables, such as PYTHONPATH, before starting python. If you are planning to use MGLTools for virtual screening only, i.e. no GUI mode, then you need to build or compile MGLTools, since only platform independent code is used for VS tutorial. You do need, however, numpy installed on your system. Here are steps needed to make sure that you can import all MGLTools packages.

1. Download any of the binary tarballs, e.g.

http://mgltools.scripps.edu/downloads/tars/releases/REL1.5.2/mgltools_i86Linux2_1.5.2.tar.gz


2. Unpack MGLToolsPckgs

   tar -xzvf mgltools_i86Linux2_1.5.2.tar.gz
   cd mgltools_i86Linux2_1.5.2
   tar -xzvf MGLToolsPckgs.tar.gz
   

3. Set PYTHONPATH environment variable.

   setenv PYTHONPATH `pwd`/MGLToolsPckgs

   How to set up PYTHONPATH on Windows?

Update: http://eflorenzano.com/blog/post/first-two-django-screencasts shows another method using symbolic links.

See also: http://autodock.scripps.edu/faqs-help/how-to/how-to-setup-adt-scripts

If you get the following warning message when starting PMV or ADT, it probably means that MSMS library is not installed.

Warning (from warnings module):
  File 
"/soft/linux/pkg/MGLTools-1.4.1/share/lib/python2.4/site-packages/Pmv/VisionInterface/PmvNodes.py", 
line 481
    warnings.warn("could not find MSMS library")
UserWarning: could not find MSMS library

• Case 1- libreadline: you are getting the following error message while running APBS:

  apbs: error while loading shared libraries: libreadline.so.4: cannot open shared object file: No such file or directory

  To fix this problem run ln -s /lib/libreadline.so.5.1 /lib/libreadline.so.4 as root.
  
• Case 2 - libg2c:
  

  apbs: error while loading shared libraries: libg2c.so.0: cannot open shared object file: No such file or directory

  Solution: install g77.
  

You can also download and build APBS from source - apbs.sourceforge.net. If you copy resulting executable to MGLToolsPckgs/binaries folder of your MGLTools installation, PMV will use that executable instead of the one shipped with MGLTools.

Case 1 - X11 is not installed.

X11 is a prerequisite for ADT/PMV and Vision. X11 can typically be found on the Mac OS X installation DVD. Scroll down in the 'Mac OS X Install disc' window and locate "Optional Installs". Double click to start the Installer, at the 'Installation Type' stage open the Applications category, select X11 and proceed. Once installed, be sure to run Software Update to obtain the latest version of X11.

• http://www.apple.com/support/downloads/x11formacosx.html

• http://developer.apple.com/opensource/tools/runningx11.html
• http://cjmart.in/2006/12/01/install-x11-on-tiger-without-the-tiger-install-dvd
  

Case 2 - BasAllloc error mesassage.

X Error of failed request:  BadAlloc (insufficient resources for  operation)
   Major opcode of failed request:  150 (GLX)
   Minor opcode of failed request:  3 (X_GLXCreateContext)
   Serial number of failed request:  1758
   Current serial number in output stream:  1759

$ defaults write com.apple.x11 enable_stereo -bool false

• http://www.apple.com/support/downloads/x11update2006113.html

adt, pmv, vision and pythonsh scripts in the bin folder check to see if /usr/lib/libGL.so.1 and /usr/X11R6/lib/libGL.so.1 are the same. These files contain your OpenGL library/driver and here is the relevant part in our scripts:

case "`uname -s`" in
...
        Linux)
                p0="/usr/lib/libGL.so.1"
                p1="/usr/X11R6/lib/libGL.so.1"
                if [ -f "$p0" -a -f "$p1" ]
                then
                        ls0=`ls -Ll "$p0" | sed 's,/.*,,'`
                        ls1=`ls -Ll "$p1" | sed 's,/.*,,'`
                        if [ "$ls0" != "$ls1" ]
                        then
                                echo "OpenGL misconfiguration detected."
                                echo "Please reinstall graphics driver."
                                #exit 1
                        fi
                fi
...

 I've commented exit part because, in most cases, adt, pmv and vision can run without any problem, even when the last if condition is true. For instance, /usr/lib/libGL.so.1 might point to a more recent version of OpenGL library, which should not stop you from running adt, pmv or vision.  The case when exit is really needed is when /usr/lib/libGL.so gets corrupted. In this case, your X server can crash when calling pmv or any other application that calls OpenGL (e.g. glxinfo). If this is the case, reinstall graphics driver.

The following page list startup problems for Chimera on i386 Linux (TclError: Togl: couldn't get visual and OpenGL misconfiguration detected) that should be useful for MGLTools users as well: http://www.cgl.ucsf.edu/chimera/1.2470/linux.html

A quick fix for this problem is to remove/comment glBlendEquationSeparateATI from your /usr/include/GL/gl.h and rebuild opengltk package. Please see Bug 834.