Downloads:
1,589
Downloads of v 4.10.0.20240522:
44
Last Update:
22 May 2024
Package Maintainer(s):
Software Author(s):
- Nicolas Guex
- Alexandre Diemand
- Manuel C. Peitsch
- and Torsten Schwede
Tags:
deepview pdbviewer chemistry protein modelingDeepView - Swiss PdbViewer
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4.10.0.20240522 | Updated: 22 May 2024
Downloads:
1,589
Downloads of v 4.10.0.20240522:
44
Maintainer(s):
Software Author(s):
- Nicolas Guex
- Alexandre Diemand
- Manuel C. Peitsch
- and Torsten Schwede
DeepView - Swiss PdbViewer 4.10.0.20240522
Legal Disclaimer: Neither this package nor Chocolatey Software, Inc. are affiliated with or endorsed by Nicolas Guex, Alexandre Diemand, Manuel C. Peitsch, and Torsten Schwede. The inclusion of Nicolas Guex, Alexandre Diemand, Manuel C. Peitsch, and Torsten Schwede trademark(s), if any, upon this webpage is solely to identify Nicolas Guex, Alexandre Diemand, Manuel C. Peitsch, and Torsten Schwede goods or services and not for commercial purposes.
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All Checks are Passing
3 Passing Tests
Deployment Method: Individual Install, Upgrade, & Uninstall
To install DeepView - Swiss PdbViewer, run the following command from the command line or from PowerShell:
To upgrade DeepView - Swiss PdbViewer, run the following command from the command line or from PowerShell:
To uninstall DeepView - Swiss PdbViewer, run the following command from the command line or from PowerShell:
Deployment Method:
This applies to both open source and commercial editions of Chocolatey.
1. Enter Your Internal Repository Url
(this should look similar to https://community.chocolatey.org/api/v2/)
2. Setup Your Environment
1. Ensure you are set for organizational deployment
Please see the organizational deployment guide
2. Get the package into your environment
Option 1: Cached Package (Unreliable, Requires Internet - Same As Community)-
Open Source or Commercial:
- Proxy Repository - Create a proxy nuget repository on Nexus, Artifactory Pro, or a proxy Chocolatey repository on ProGet. Point your upstream to https://community.chocolatey.org/api/v2/. Packages cache on first access automatically. Make sure your choco clients are using your proxy repository as a source and NOT the default community repository. See source command for more information.
- You can also just download the package and push it to a repository Download
-
Open Source
-
Download the package:
Download - Follow manual internalization instructions
-
-
Package Internalizer (C4B)
-
Run: (additional options)
choco download deepview --internalize --source=https://community.chocolatey.org/api/v2/
-
For package and dependencies run:
choco push --source="'INTERNAL REPO URL'"
- Automate package internalization
-
Run: (additional options)
3. Copy Your Script
choco upgrade deepview -y --source="'INTERNAL REPO URL'" [other options]
See options you can pass to upgrade.
See best practices for scripting.
Add this to a PowerShell script or use a Batch script with tools and in places where you are calling directly to Chocolatey. If you are integrating, keep in mind enhanced exit codes.
If you do use a PowerShell script, use the following to ensure bad exit codes are shown as failures:
choco upgrade deepview -y --source="'INTERNAL REPO URL'"
$exitCode = $LASTEXITCODE
Write-Verbose "Exit code was $exitCode"
$validExitCodes = @(0, 1605, 1614, 1641, 3010)
if ($validExitCodes -contains $exitCode) {
Exit 0
}
Exit $exitCode
- name: Install deepview
win_chocolatey:
name: deepview
version: '4.10.0.20240522'
source: INTERNAL REPO URL
state: present
See docs at https://docs.ansible.com/ansible/latest/modules/win_chocolatey_module.html.
chocolatey_package 'deepview' do
action :install
source 'INTERNAL REPO URL'
version '4.10.0.20240522'
end
See docs at https://docs.chef.io/resource_chocolatey_package.html.
cChocoPackageInstaller deepview
{
Name = "deepview"
Version = "4.10.0.20240522"
Source = "INTERNAL REPO URL"
}
Requires cChoco DSC Resource. See docs at https://github.com/chocolatey/cChoco.
package { 'deepview':
ensure => '4.10.0.20240522',
provider => 'chocolatey',
source => 'INTERNAL REPO URL',
}
Requires Puppet Chocolatey Provider module. See docs at https://forge.puppet.com/puppetlabs/chocolatey.
4. If applicable - Chocolatey configuration/installation
See infrastructure management matrix for Chocolatey configuration elements and examples.
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This package was approved by moderator Windos on 23 May 2024.
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.
$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)
}
Log in or click on link to see number of positives.
- SPDBV_4.10_PC.zip (369c0c9b6e05) - ## / 66
- deepview.4.10.0.20240522.nupkg (a130b42aaa91) - ## / 68
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.
Add to Builder | Version | Downloads | Last Updated | Status |
---|---|---|---|---|
DeepView - Swiss PdbViewer 4.10.0.20240522 | 44 | Wednesday, May 22, 2024 | Approved | |
DeepView - Swiss PdbViewer 4.10.0.20161116 | 1065 | Wednesday, November 16, 2016 | Approved | |
DeepView - Swiss PdbViewer 4.10 | 480 | Wednesday, April 27, 2016 | Approved |
Copyright © 1995-2012 Nicolas Guex
This package has no dependencies.
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