Saturday, July 3, 2010

Running Swiss-PdbViewer on Ubuntu

Swiss-PdbViewer in Ubuntu using Wine.

Introduction to Swiss-PdbViewer

DeepView – Swiss-PdbViewer (or SPDBV) is an bioinformatics application that provides a user friendly graphical interface allowing to view and analyze protein and nucleic acid structure. This program is associated with Swiss-Model (an automated homology modeling server running in the Geneva Glaxo Welcome Experimental Research), accessible via the ExPASy web server. Through this application, proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. Working with these two programs greatly reduces the amount of work necessary to generate models, as it is possible to thread a protein primary sequence onto a 3D template and get an immediate feedback of how well the threaded protein will be accepted by the reference structure before submitting a request to build missing loops and refine sidechain packing.

Swiss-PdbViewer can also read electron density maps, and provides various tools to build into the density. In addition, various modeling tools are integrated and command files for popular energy minimization packages can be generated.

Currently Swiss-PdbViewer is released for Microsoft Windows and Macintosh OS. In order to run Swiss-PdbViewer in Ubuntu OS, a windows application loader WINE must be installed.

What is Wine?

Wine is an implementation of Windows APIs on top of X and Unix. Think of Wine as a Windows compatibility layer. Wine provides a program loader, allowing many unmodified Windows binaries to run under Intel Unixes. Wine works on most popular Intel Unixes, including Linux, FreeBSD, and Solaris.

In Linux Ubuntu OS, Wine can be easily installed through Ubuntu Software Center.

Steps to install Wine

To install Wine, simply follow these steps.

1. Go to ApplicationsUbuntu Software Center.

Ubuntu Software Center

2. Click the tab All.

3. In the search bar type keyword “wine”.

Wine in Ubuntu

4. Select the hit Wine and press Install button.

5. Wine will be installed.

Wine in Ubuntu Screenshot.

Steps to run SPDBV through Wine

1. Download the windows compatible Swiss-PdbViewer application from SPDBV download site and decompress it.

2. Open the decompressed folder. Right click the application spdbv.exe and open with Wine Windows Program Loader.

Swiss-PdbViewer Folder.

Other bioinformatics tools such as RasMol, Clustal X, TreeView, SeaView, PyMOL, Cn3D, EMBOSS, fastDNAml, etc can be installed instantly through Ubuntu Software Center.

Note: You must be on-line while installing the application.

0 comments :

Post a Comment