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How to install DeepView-Swiss PDB Viewer on Linux?

Tariq Abdullah

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DeepView (Swiss-PDB Viewer) [1] is used to analyze multiple proteins simultaneously. Protein structure alignment, active site comparison, amino acid mutations, H-bonds, and other relevant functions can be easily performed using this software [1]. In this article, we will install DeepView on Linux (Ubuntu).

Preparing

At first, update and upgrade your system using the following commands:

$ sudo apt-get update
$ sudo apt-get upgrade

Downloading

Download the software from here or use the command line as shown below:
$ sudo wget http://www.genebee.msu.su/spdbv/program/spdbv37sp5-Linux.tar.gz

Installing

Open a terminal and change to the directory where you have downloaded the software. Let’s say here it is ‘Downloads’.

$ cd Downloads

$ tar xvf spdbv37sp5-Linux.tar

$ ./install.sh

Sometimes, an error may occur regarding the loading of shared libraries, libMesaGL.so.3. These libraries are linked with DeepView which are now called libGL.so.3 and libGLU.so instead of libMesaGL.so and libMesaGLU.so.

If you encounter this error, then make some symbolic links to the old names as shown below: (Locate the libraries in your system, it is assumed here that these libraries are present in /usr/lib/.)

$ ln -s /usr/lib/libGL.so.1.2.0 /usr/lib/libMesaGL.so.3

$ ln -s /usr/lib/libGLU.so.1.2.0 /usr/lib/libMesaGLU.so.3

 

References

  1. Kaplan, W., & Littlejohn, T. G. (2001). Swiss-PDB viewer (deep view). Briefings in bioinformatics2(2), 195-197.

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

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