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UCSF Chimera

1.13

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This package was approved by moderator gep13 on 8/8/2018.

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, nonprofit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics (RBVI), funded by the National Institutes of Health (NIGMS P41-GM103311).

Non-Commercial use ONLY

Use of the Chimera is restricted to non-commercial, personal, academic, non-profit, or government-sponsored research purposes. Commercial use of the Software requires a separately executed written license agreement.

To install UCSF Chimera, run the following command from the command line or from PowerShell:

C:\> choco install chimera

To upgrade UCSF Chimera, run the following command from the command line or from PowerShell:

C:\> choco upgrade chimera

Files

Hide
  • tools\chocolateyinstall.ps1 Show
    $ErrorActionPreference = 'Stop'
    
    $BaseURL = 'https://www.cgl.ucsf.edu'
    
    # Discovering download link
    # Process found here:  https://stackoverflow.com/questions/34422255/
    # Unsure if all settings are needed.
    $url = "$BaseURL/chimera/cgi-bin/secure/chimera-get.py"
    $postData = "choice=Accept&file=win64/chimera-$env:ChocolateyPackageVersion-win64.exe"
    $buffer = [text.encoding]::ascii.getbytes($postData)
    [net.httpWebRequest] $req = [net.webRequest]::create($url)
    $req.method = "POST"
    $req.Accept = "text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8"
    $req.Headers.Add("Accept-Language: en-US")
    $req.Headers.Add("Accept-Encoding: gzip,deflate")
    $req.Headers.Add("Accept-Charset: ISO-8859-1,utf-8;q=0.7,*;q=0.7")
    $req.AllowAutoRedirect = $false
    $req.ContentType = "application/x-www-form-urlencoded"
    $req.ContentLength = $buffer.length
    $req.TimeOut = 50000
    $req.KeepAlive = $true
    $req.Headers.Add("Keep-Alive: 300");
    $reqst = $req.getRequestStream()
    $reqst.write($buffer, 0, $buffer.length)
    $reqst.flush()
    $reqst.close()
    [net.httpWebResponse] $res = $req.getResponse()
    $resst = $res.getResponseStream()
    $sr = new-object IO.StreamReader($resst)
    $result = $sr.ReadToEnd()
    $res.close()
    
    $URLstub = ($result.split() |? {$_ -match 'href='}) -replace '.*href="(.*)".*','$1'
    
    Write-Host 'You are establishing a license agreement as defined here:' -ForegroundColor Cyan
    Write-Host 'http://www.cgl.ucsf.edu/chimera/license.html' -ForegroundColor Cyan
    
    $packageArgs = @{
       packageName   = $env:ChocolateyPackageName
       fileType      = 'EXE'
       url64bit      = $BaseURL + $URLstub
       softwareName  = 'UCSF Chimera*' 
       checksum64    = '4b6d567e1f51ee6523cee85973ed627346e82f828eb987b0dbac90e33755b4cd'
       checksumType64= 'sha256'
       silentArgs   = '/VERYSILENT /SUPPRESSMSGBOXES /NORESTART /SP-'
       validExitCodes= @(0)
    }
    
    Install-ChocolateyPackage @packageArgs
    
  • tools\LICENSE.txt Show
    From: http://www.cgl.ucsf.edu/chimera/license.html
    
    LICENSE
    
    UCSF Chimera Non-Commercial Software License Agreement
    
    This license agreement ("License"), effective today, is made by and 
    between you ("Licensee") and The Regents of the University of California, 
    a California corporation having its statewide administrative offices at 
    1111 Franklin Street, Oakland, California 94607-5200 ("The Regents"), 
    acting through its Office of Innovation, Technology & Alliances, 
    University of California San Francisco ("UCSF"), 3333 California Street, 
    Suite S-11, San Francisco, California 94143, and concerns certain software 
    known as "UCSF Chimera," a system of software programs for the 
    visualization and interactive manipulation of molecular models, developed 
    by the Computer Graphics Laboratory at UCSF for research purposes and 
    includes executable code, source code, and documentation ("Software").
    
    1. General. 
       A non-exclusive, nontransferable, perpetual license is granted to the 
       Licensee to install and use the Software for academic, non-profit, or 
       government-sponsored research purposes. Use of the Software under this 
       License is restricted to non-commercial purposes. Commercial use of 
       the Software requires a separately executed written license agreement.
    2. Permitted Use and Restrictions. 
       Licensee agrees that it will use the Software, and any modifications, 
       improvements, or derivatives to the Software that the Licensee may 
       create (collectively, "Improvements") solely for internal, non-
       commercial purposes and shall not distribute or transfer the Software 
       or Improvements to any person or third parties without prior written 
       permission from The Regents. The term "non-commercial," as used in 
       this License, means academic or other scholarly research which (a) is 
       not undertaken for profit, or (b) is not intended to produce works, 
       services, or data for commercial use, or (c) is neither conducted, nor 
       funded, by a person or an entity engaged in the commercial use, 
       application or exploitation of works similar to the Software.
    3. Ownership and Assignment of Copyright. 
       The Licensee acknowledges that The Regents hold copyright in the 
       Software and associated documentation, and the Software and associated 
       documentation are the property of The Regents. The Licensee agrees 
       that any Improvements made by Licensee shall be subject to the same 
       terms and conditions as the Software. Licensee agrees not to assert a 
       claim of infringement in Licensee copyrights in Improvements in the 
       event The Regents prepares substantially similar modifications or 
       derivative works. The Licensee agrees to use his/her reasonable best 
       efforts to protect the contents of the Software and to prevent 
       unauthorized disclosure by its agents, officers, employees, and 
       consultants. If the Licensee receives a request to furnish all or any 
       portion of the Software to a third party, Licensee will not fulfill 
       such a request but will refer the third party to the UCSF Chimera web 
       page so that the third party's use of this Software will be subject 
       to the terms and conditions of this License. Notwithstanding the 
       above, Licensee may disclose any Improvements that do not involve 
       disclosure of the Software.
    4. Copies. 
       The Licensee may make a reasonable number of copies of the Software 
       for the purposes of backup, maintenance of the Software or the 
       development of derivative works based on the Software. These 
       additional copies shall carry the copyright notice and shall be 
       controlled by this License, and will be destroyed along with the 
       original by the Licensee upon termination of the License.
    5. Acknowledgement. 
       Licensee agrees that any publication of results obtained with the 
       Software will acknowledge its use by an appropriate citation as 
       specified in the documentation.
    6. Disclaimer of Warranties and Limitation of Liability. 
       THE LICENSEE AGREES THAT ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, 
       BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND 
       FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. THE REGENTS MAKES NO 
       REPRESENTATION OR WARRANTY THAT THE SOFTWARE WILL NOT INFRINGE ANY 
       PATENT OR OTHER PROPRIETARY RIGHT. IN NO EVENT SHALL THE REGENTS BE 
       LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
       CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
       SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR 
       BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
       WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE 
       OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, 
       EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
    7. Termination. 
       This License is effective until terminated by either party. Licensee's 
       rights under this License will terminate automatically without notice 
       from The Regents if Licensee fails to comply with any term(s) of this 
       License. Licensee may terminate the License by giving written notice 
       of termination to The Regents. Upon termination of this License, 
       Licensee shall immediately discontinue all use of the Software and 
       destroy the original and all copies, full or partial, of the Software, 
       including any modifications or derivative works, and associated 
       documentation.
    8. Governing Law and General Provisions. 
       This License shall be governed by the laws of the State of California, 
       excluding the application of its conflicts of law rules. This License 
       shall not be governed by the United Nations Convention on Contracts 
       for the International Sale of Goods, the application of which is 
       expressly excluded. If any provisions of this License are held invalid 
       or unenforceable for any reason, the remaining provisions shall remain 
       in full force and effect. This License is binding upon any heirs and 
       assigns of the Licensee. The License granted to Licensee hereunder may 
       not be assigned or transferred to any other person or entity without 
       the express consent of The Regents. This License constitutes the 
       entire agreement between the parties with respect to the use of the 
       Software licensed hereunder and supersedes all other previous or 
       contemporaneous agreements or understandings between the parties, 
       whether verbal or written, concerning the subject matter. Any 
       translation of this License is done for local requirements and in the 
       event of a dispute between the English and any non-English versions, 
       the English version of this License shall govern. 
    
    Revised 28jan04
    

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Dependencies

This package has no dependencies.

Package Maintainer(s)

Software Author(s)

  • UCSF Resource for Biocomputing
  • Visualization
  • and Informatics

Copyright

© The Regents of the University of California, 1999-2017

Tags

Release Notes

https://www.cgl.ucsf.edu/chimera/docs/relnotes.html

Version History

Version Downloads Last updated Status
UCSF Chimera 1.12 129 Thursday, February 22, 2018 approved

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