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EBI Groups Thornton Software LigPlot+

LigPlot+ Installation Instructions

Instructions for downloading LigPlot+ will be sent to you by e-mail when you return the signed Confidentiality Agreement.
If you belong to a non-academic institution, download instructions will be sent when you have a licence for the program.

If you do not have the programs, see the LigPlot+ home page for information on obtaining them.

Download and install JRE

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.

 

Install LigPlot+

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

1a. Windows

On a Windows machine, appropriate directories might be:
C:\      

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

You can use WinZip to unzip all the files into your chosen directory. This will create a directory called LigPlus and various subdirectories beneath that.

Non-academic users will need a licence file, called licence.txt. You will have been sent this file by e-mail. It needs to be saved in the subdirectory LigPlus/lib/params.

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

Under linux, simply move the LigPlus.tar.gz file to the appropriate destination and then gunzip and untar it as follows:
gunzip LigPlus.tar.gz
tar -xvf LigPlus.tar
Again. this will create a directory called LigPlus and various subdirectories beneath that.

Non-academic users will need a licence file, called licence.txt. You will have been sent this file by e-mail. It needs to be saved in the subdirectory LigPlus/lib/params.

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 gives instructions on how to complete this form (see the Paths and directories section).

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

In linux, 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.

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

 

 

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