How do I install LIGPLOT Plus on 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.
Is LIGPLOT a free software?
Available free. To receive a licenced version of the programs, please go to: Academic licence.
Why LIGPLOT is not working?
LIGPLOT doesn’t work on my docked structure The most likely reason is that your PDB file is not in the correct PDB format. It is quite astonishing how many well-known docking programs seem unable to output a correctly formatted PDB file – particularly for the ligand atoms.
How do I download LigPlus?
Download the software by going to http://www.ebi.ac.uk/thornton-srv/software/LigPlus/download.html and install it. It LigPlus fails to generate the schematics the it is likely that your PDB file is not following the PDB conventions. Use the ‘Structure Conversion function of Simulaid to ‘Regularize’ your PDB file.
How do you run a LIGPLOT?
The procedure is as follows: run NACCESS on your PDB file and then run LIGPLOT on the . asa file generated by NACCESS. Make sure that the option for showing accessibility shading is set to Y in the ligplot. prm parameter file.
How do you use LIGPLOT plus?
Clicking on the LIGPLOT or DIMPLOT tabs allows you to choose which of the two programs to run.
- LIGPLOT. Select which ligand you wish to plot from the list.
- DIMPLOT. Select which protein chain pair you would like plotted, or enter the residue ranges of the chains or domains you want to plot.
How do you use Ligplot plus?
What is LIGPLOT used for?
In bioinformatics, LIGPLOT is a computer program that generates schematic 2-D representations of protein-ligand complexes from standard Protein Data Bank file input. The LIGPLOT is used to generate images for the PDBsum resource that summarises molecular structure.
What is LIGPLOT+?
LIGPLOT+ The original software for 2D representations of Ligand-Binding site interactions. Ligplot+ This is the original software for 2D representations of Ligand-Binding site interactions. With the latest version you can also flexibly compare:
How to convert LIGPLOT+ to an image file?
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 .
How do I run LIGPLOT+ on 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.
How do I start LIGPLOT+ from a DRW file?
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.