248

Downloads

138

Downloads of v 4.10.0.20161116

11/16/2016

Last update

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

Hide

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)
}

Virus Scan Results

libcurl.dll (43673252f611) - ## / 54 - Log in or click on link to see number of positives
spdbv.exe (f85ff6d662f8) - ## / 55 - Log in or click on link to see number of positives
SPDBV_4.10_PC.zip (369c0c9b6e05) - ## / 56 - Log in or click on link to see number of positives
deepview.4.10.0.20161116.nupkg (75494079ff5a) - ## / 56 - Log in or click on link to see number of positives

In cases where actual malware is found, the packages are subject to removal. Software sometimes has false positives. Moderators do not necessarily validate the safety of the underlying software, only that a package retrieves software from the official distribution point and/or validate embedded software against official distribution point (where distribution rights allow redistribution).

Chocolatey Pro provides runtime protection from possible malware.

Dependencies

This package has no dependencies.

Maintainer(s)

teknowledgist

Software Author(s)

Nicolas Guex
Alexandre Diemand
Manuel C. Peitsch
and Torsten Schwede

Copyright

Version History

Version	Downloads	Last updated	Status
DeepView - Swiss PdbViewer 4.10.0.20161116	138	Wednesday, November 16, 2016	approved
DeepView - Swiss PdbViewer 4.10	110	Wednesday, April 27, 2016	approved

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