LigPlot+ v.1.4 a Graphical User Interface for the LIGPLOT and DIMPLOT programs
LigPlot+ is a graphical front-end to the LIGPLOT and DIMPLOT programs.
- LIGPLOT - automatically generates schematic diagrams of protein-ligand interactions for a given ligand in a PDB file.
- DIMPLOT - plots interactions across a selected protein-protein or domain-domain interface.
Whilst this application is supported under Windows and Linux there is no official support for Mac OS X, however since the GUI LigPlot is written in java and LIGPLOT is written in C there seems to be no reason why it should not run under Mac OS X. I was kindly supplied access to the program and after downloading I put the LigPlus folder in my applications folder and started the application by typing this command in the Terminal
java -jar /Applications/LigPlus/LigPlus.jar
This opens the application and the first time you need to define a few paths. The only one I needed to modify was the path to the PyMOL executable, if I simply put the path to the app in the Applications folder I got and error that “MacPyMOL was a folder”. If you right-click on MacPyMOL and select “Show Package contents” you can get the path to the actual executable. When I entered this as shown below it seemed to work fine.
To read in a pdb file simply select “Open” from the file menu
Select the ligand you want to generates schematic diagram of the protein-ligand interactions for the selected ligand in the PDB file. In a few seconds the plot will be generated as shown below.
The buttons at the bottom allow you to modify the display style, change the colour of atoms and bonds or the types of interactions highlighted. You can rotate a residue about any of its atoms by right-clicking on the atom you want to pivot about. A marker will appear over the selected atom to identify it then drag another atom in the residue. This is useful if you want to manually modify the schematic. You can also edit any of the text labels on the plot by selecting the text item by right-clicking on it. A box containing the text string will appear. You can edit the text as required.
If you click on the PyMOL button the structure is then opened in PYMOL
The full manual is in LigPlus/lib/docs/manual.html. See Also Laskowski R A, Swindells M B (2011). LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J. Chem. Inf. Model., 51, 2778-2786. 10.1021/ci200227u">DOI
In summary with a couple of minor tweaks this seems to run happily on my machine under Mac OS X 10.8.4
Last Updated 9 June 2013