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DeepView - Swiss PdbViewer

4.10.0.20161116

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This package was approved by moderator flcdrg on 11/24/2016.

Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The 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.

Swiss-PdbViewer (aka DeepView) has been developped since 1994 by Nicolas Guex. Swiss-PdbViewer is tightly linked to SWISS-MODEL, an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB) at the Structural Bioinformatics Group at the Biozentrum in Basel.

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 residues can be mutated.

Finally, as a special bonus, POV-Ray scenes can be generated from the current view in order to make stunning ray-traced quality images. An example can be found here.

To install DeepView - Swiss PdbViewer, run the following command from the command line or from PowerShell:

C:\> choco install deepview

To upgrade DeepView - Swiss PdbViewer, run the following command from the command line or from PowerShell:

C:\> choco upgrade deepview

Files

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  • tools\chocolateyInstall.ps1 Show
    $packageName = 'deepview'
    
    $InstallDir = Split-path (Split-path $MyInvocation.MyCommand.Definition)
    
    $InstallArgs = @{
       PackageName = $packageName
       Url = 'http://spdbv.vital-it.ch/download/binaries/SPDBV_4.10_PC.zip' 
       UnzipLocation = $InstallDir
       checkSum = '369C0C9B6E058BB67C86DC24D711D6A655E5E023D639FCDA13EC2FE272DE1858'
       checkSumType = 'sha256'
    }
    Install-ChocolateyZipPackage @InstallArgs
    
    $target   = Join-Path $InstallDir 'SPDBV_4.10_PC\spdbv.exe'
    $shortcut = Join-Path ([System.Environment]::GetFolderPath('Desktop')) 'Swiss-PdbViewer.lnk'
    
    Install-ChocolateyShortcut -ShortcutFilePath $shortcut -TargetPath $target
    
    
  • tools\chocolateyUninstall.ps1 Show
    $desktop = ([System.Environment]::GetFolderPath('Desktop'))
    $shortcut = Join-Path $desktop 'Swiss-PdbViewer.lnk'
     
    if ([System.IO.File]::Exists($shortcut)) {
        Write-Debug "Found the desktop shortcut. Deleting it..."
        [System.IO.File]::Delete($shortcut)
    }

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Dependencies

This package has no dependencies.

Maintainer(s)

Software Author(s)

  • Nicolas Guex
  • Alexandre Diemand
  • Manuel C. Peitsch
  • and Torsten Schwede

Copyright

Copyright © 1995-2012 Nicolas Guex

Tags

Version History

Version Downloads Last updated Status
DeepView - Swiss PdbViewer 4.10 89 Wednesday, April 27, 2016 approved

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