LeView (Ligand Environment Viewer) is a Java program that can be used to generate 2D representations of ligands and their environments and binding interactions for PDB entries. The program can be used automatically (in command line) or interactively (with a graphical interface) – in the latter case, you can customise the display in a variety of ways. The views you create can be saved in several different graphics formats (PNG, JPEG, GIF, PDF, SVG, EPS). The list of the interactions represented in the diagram, with the atoms involved and the associated distance, can also be exported as flat text.
Overview
LeView automatically detects ligands and ions from the PDB entry and shows you the complete list. You can also specify the ligand by entering an appropriate residue range. Diagram can be customised by changing the cut-off distance for hydrogen bonds and nearby residues. Possible water-mediated hydrogen bonds can be added to the diagrams. The diagram can also be manipulated by moving elements (with interactive version) or by choosing the element colour and style.
Diagram generated by LeView for PDE5 inhibitor (1udt).
Ligand appears in black, hydrogen bonds in blue and close residues are represented by colored ovals depending on hydrophobic properties.
Installation and usage
LeView does not need installation step but require Java installed on your machine.
Please make sure you have a Java Runtime Environment (JRE) installed and enabled.
To install Java, visit this page.
To run LeView in interactive version, just double click on the corresponding icon.
To run LeView in command line version, use the following command line:
java -jar LeViewLine.jar PDB_entry
See manual for more details.
LeView uses the VectorGraphics package of the FreeHEP Java Library and the ftp4j library for FTP download.
New release
In the new release of LeView, the type of chemical bonds (e.g. double bonds) are identified downloading the residue mmcif files located at the PDBe FTP site (ftp.ebi.ac.uk) using the ftp4j library. If you do not have an internet connexion, all the chemical bonds will be considered as single bonds.
Download
You can freely download LeView:
- Interactive version with graphical interface: LeView (for all OS) or Windows.exe
- Manual for interactive version
- Command Line version: LeViewLine
- Manual for command line version
Source code is available under GNU General Public Licence.
- Source code of LeView (with graphical interface): LeView-src
- Source code of LeViewLine: LeViewLine-src
About LeView
LeView was developed by Ségolène Caboche during its post-doc position at European Bioinformatics Institute in the PDBe Team, led by Prof. Gerard Kleywegt.
Thanks to the EBI for funding and to PDBe staff for help, testing and discussions.
For questions about LeView or for bug reports, please contact Ségolène Caboche (segolene.caboche<AT>pasteur-lille.fr)
Archives
- LeView (for all OS) or Windows.exe
- Command Line version: LeViewLine
- Source code of LeView (with graphical interface): LeView-src
- Source code of LeViewLine: LeViewLine-src