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EBI Groups Thornton Software LigPlot+

LigPlot+ Installation Instructions

These instructions assume you have downloaded the LigPlus.zip file and saved it in a suitable directory. Please follow them carefully, and note the list of "Common problems" at the end.

If you don't have the file, please go to the LigPlot+ home page for information on obtaining it.

Download and install JRE

To run LigPlot+ you will need the most recent version of the Java runtime environment from Sun:

Java SE Runtime Environment (JRE)

Follow the appropriate installation instructions in the documentation on the downloads page.

Please note, Sun Java is the preferred option as other versions of Java (eg OpenJDK or GCJ) may lack some of the classes that LigPlot+ requires.

 

Install LigPlot+

The LigPlot+ executables and associated files are in a single zip file, LigPlus.zip. Save the file in the directory where you wish the executables to be stored.

1a. Windows

On a Windows machine, an appropriate directory might be:
C:\

(Note that installation in the C:\Program Files directory may cause problems on some systems as you may need to have admin permission to install here and also whenever you edit the program parameters).

Right-click on the file's icon and select "Extract All". When prompted, choose to extract to C:\.

This will create a directory called C:\LigPlus and put all the program files in that directory.

Desktop icon


  You can create a desktop icon as follows. Go to the directory where you installed the executables and find the LigPlus.jar file. Right-click on it and select the "Create Shortcut" option. This will create a new file called LigPlus - Shortcut (although the exact name depends on which version of Windows you have).
  Move this new file to your desktop. You can now edit the name so that it reads LigPlus or LigPlot+. Right-click on the icon and select the "Properties" option. Now click the "Change icon" button and then use the "Browse" button to select the icon file: LigPlus/lib/images/ligplus.ico. Finally, press "OK" twice, and the icon should appear on your desktop.

Auto-load .drw files


  The plots generated by LigPlot+ are saved as files with .drw extensions. You can set up your system so that double-clicking on a .drw file automatically starts LigPlot+ with that plot loaded. The steps are as follows:
 
  1. Right-click on a .drw file.
  2. Select the Open with option.
  3. Ensure the "Always use the selected program to open this kind of file" box is ticked.
  4. Click the Browse button.
  5. Locate the cLigPlus.bat file in you LigPlus directory and select it either by double-clicking it, or by clicking on the Open icon.
  6. Click the OK button.
Important note. If you have installed LigPlot+ in any directory other that C:\LigPlus, you will first need to edit the cLigPlus.bat file (which contains only a single line) to change the path to the LigPlus.jar file accordingly. Remember that, if there is a space in a directory name (eg C:\Program Files), you need to prefix the space with a backslash (ie C:\Program\ Files) when you edit the cLigPlus.bat file.

1b. Linux and mac

Under linux, simply move the LigPlus.zip file to the appropriate destination and then unzip it as follows:
unzip LigPlus.zip
Again. this will create a directory called LigPlus and various subdirectories beneath that.

Note for mac users

LigPlot+ calls a number of executables to perform its processing. Some versions of the mac OS will only run 64-bit executables, while others will only run 32-bit executables. LigPlot+ has both versions, but under some versions of the OS, LigPlot+ tries to call the wrong ones. So, if you get a message such as "No ligplot.drw file found", the most likely reason is that the incorrect executable has been run.

The solution is to do the following:

  1. Go to the LigPlus directory where you installed the program. You will see a subdirectory called lib.
  2. Go into the lib subdirectory.
  3. Among the directories there, you will see two called
    • exe_mac
    • exe_mac64
    The first contains the old, 32-bit executables, while the second has a set of 64-bit executables. (If the latter is not there, you may have downloaded the old version of the programs (v.1.4) - in which case you will need to download v.2.1).
  4. Go into each of these executable directories in turn and try running the ligplot executable by:
    ./ligplot
    If the operating system is happy with it, you should get the message:
    *** ERROR. No command-line arguments entered!
    If not, you'll get some gibberish like "lazy symbol binding failed" or "Abort trap".

    Having identified the directory with the working version, copy its contents to the other one. Then try running LigPlot+ again.

2. After installation

Run LigPlot+ as described below. The first time you run the program you will need to configure it for your system. An entry-form will pop up so that you can supply the locations on your system of: PDB files, the Het Group Dictionary, the RasMol program (if you have it), and so on. The Operating Manual (see below) gives instructions on how to complete this form (see the Paths and directories section).

Operating Manual

The LigPlot+ Operating Manual is supplied in HTML format, so can be viewed in any web browser. You will find it in the directory LigPlus/lib/docs. Just load the file called manual.html.

Alternatively, you can get the same manual from within LigPlot+ by clicking Help from the menu bar and then selecting Manual.

There is also a version of the manual on the LigPlot+ website at: Operating Manual.

Note for linux users

If the program has been installed in a directory with admin-only access, this first run will need to be performed by someone with permission to write files in that directory as the parameters need to be written to the LigPlus/lib/params/ligplus.par file.

After this, users with no access to that directory can change (and save) any of the program parameters only if they have their own copy of the parameter file (ligplus.par) in their current directory when they start LigPlot+.

 

Running LigPlot+

1a. Windows

On a Windows machine, double-click on LigPlus.jar in the LigPlus directory (or on the shortcut icon on your Desktop if you've set one up). When the program has loaded you will see the starting LIGPLOT+ window. See the Operating Manual for instructions on how to generate a LIGPLOT/DIMPLOT diagram.

Alternatively, you can double-click on the cLigPlus.bat file in the LigPlus directory. This will open up a command window beofre starting LigPlot+. The window shows all the debugging information that the program produces, which could be helpful if you encounter a problem.

1b. Linux and mac

In linux and mac, LIGPLOT+ is run by:
java   -cp   [path]   -jar   [path]LigPlus.jar
where [path] is the directory where the LigPlus.jar file is.

To make your life easier, you can create an alias for the above command in your .cshrc file. For example:

alias   ligplus   'java   -cp   /usr/bin/LigPlus/   -jar   /usr/bin/LigPlus/LigPlus.jar'

Once the .cshrc file has been sourced (eg when you next open a terminal) simply typing ligplus will start the program. You can also start the program by typing: ligplus file.drw, where file.drw is the name of a plot you have previously saved. This command will start LIGPLOT+ with the specified plot displayed.

Z shell

If you uae the Z shell on your mac, modify the .zshrc file, rather than the .cshrc file, in the instructions above.

bash users

Note that, if you have bash, you need to use export instead of alias, and add it to your .bashrc file, as follows:

export ligplus='java   -cp   /usr/bin/LigPlus/   -jar   /usr/bin/LigPlus/LigPlus.jar'
Then, to start LIGPLOT+, type $ligplus (with the dollar at the front).

2. Generating a LIGPLOT/DIMPLOT diagram

See the Operating Manual for instructions on how to generate a LIGPLOT/DIMPLOT diagram.

Note that, LIGPLOT+ outputs PostScript files, so if you need an image file, you will need to use a suitable package to do so. Some software suggestions are:

  • On Windows, you can install GSview which can convert to several image formats.
  • Under linux, you can use the convert program from ImageMagick.
  • If you have Ubuntu, you can obtain a free script called convertPS from Dr N Hari by writing to hari.crmr@gmail.com.

 

Common problems

ligplot.drw file not found

There can be several reasons for this error.
  1. The most likely reason is that the temporary directory defined in the LigPlot+ Program Paths and Directory parameters is missing. LigPlot+ requires this directory for its working files, and it cannot run without it. Please see Section 2 (Paths and Directories) of the Operating Manual. You either need to create a directory with the same name as is defined in the parameters, or change the name of the temporary directory in the parameters to one that exists.

  2. On macs, this error can occur when LigPlot+ is trying to access the wrong set of executable files. Please see the "Note for mac users" in section 1b above.

  3. Finally, if the PDB file you are trying to plot is in the wrong format, or somehow unreadable, the program will be unable to generate a plot.