Deep View Course Manual

Deep View Course Manual - Babraham Bioinformatics Viewing...

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Viewing Protein 3D Structures with Deep View A quick guide to the visualisation components of Deep View Version 1.3 (public) Babraham Bioinformatics
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Viewing Protein 3D Structures with Deep View 2 Licence This manual is © 2007-8, Simon Andrews. This manual is distributed under the creative commons Attribution-Non-Commercial-Share Alike 2.0 licence. This means that you are free: to copy, distribute, display, and perform the work to make derivative works Under the following conditions: Attribution. You must give the original author credit. Non-Commercial. You may not use this work for commercial purposes. Share Alike. If you alter, transform, or build upon this work, you may distribute the resulting work only under a licence identical to this one. Please note that: For any reuse or distribution, you must make clear to others the licence terms of this work. Any of these conditions can be waived if you get permission from the copyright holder. Nothing in this license impairs or restricts the author's moral rights. Full details of this licence can be found at http://creativecommons.org/licenses/by-nc-sa/2.0/uk/legalcode
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Viewing Protein 3D Structures with Deep View 3 Introduction Whilst much useful information about a protein can be derived from looking at both DNA and protein sequence information the only way to get a complete understanding of its function is by looking at its 3D structure. Proteins operate in a 3D environment and by looking at them in this context it is possible to explain observations which could not be accounted for by other analyses. There are now a huge number of protein structures made publicly available through the protein data bank (PDB). In this course you will be shown how to access these structures and manipulate them on your own computer. Deep View The basis for this course is a software package called Deep View (formerly called the Swiss PDB Viewer). This is a free package written by a group at the Swiss Institute for Bioinformatics. It is a pretty comprehensive molecular modelling package providing a variety of visualisation options as well as allowing homology modelling and energy minimisation. It also interacts with the POV-Ray raytracing package to produce publication quality molecular graphics. This course will not cover the homology modelling aspects of Deep View, but will demonstrate how to use the visualisation components to analyse both single and multiple structures. You can download Deep View from http://spdbv.vital-it.ch/
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Viewing Protein 3D Structures with Deep View 4 Basic Deep View Controls Starting Deep View Deep View is started by double-clicking the icon after installation. You should see a splash screen appear. Clicking on this will make it go away, and will leave you with the main program toolbar.
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This note was uploaded on 01/03/2012 for the course BI 170a taught by Professor List during the Fall '09 term at Caltech.

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Deep View Course Manual - Babraham Bioinformatics Viewing...

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