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Revised 01/25/2013

CDTree 3.1 is available for Windows and Intel-based Macintosh computers.

The CDTree 3.1 installation includes Cn3D 4.3, a 3D structure viewer and multiple sequence alignment editor also developed at NCBI and which can exchange data with CDTree. The Cn3D home page provides additional information about the program's features and functions as well as a tutorial. (Note that the older release, Cn3D 4.1, is not able to communicate with CDTree.)

Both Cn3D and CDTree can be launched from various links on Conserved Domain Database, MMDB, and other NCBI web pages (for example, see the test links for the PC and Mac below). Below are the file extension and MIME-type associations for these two programs.

File Extension MIME Type
Cn3D .cn3 chemical/ncbi-asn1-binary
CDTree .cn4 chemical/ncbi-asn1-cddproject


While Cn3D can not read CDTree project files, CDTree can import individual 'conserved domain' or CD files with the .cn3 extension. Many files from earlier versions of Cn3D and CDTree 3.0 are readable by CDTree 3.1, but this is not guaranteed in all cases.


Distribution Contents

  1. CDTree 3.1
  2. Cn3D 4.3
  3. fa2cd.exe (command-line utility to convert mFASTA files into CDTree and Cn3D readable CD files)
CDTree Readme
Release Notes



 
PC Installation

Download the CDTree 3.1 software distribution using the link appropriate to your PC's operating system.
  • Windows XP/Vista/Windows 7 (or if your Windows machine has the current Windows Installer software):

    Windows 7 installation note: Users without administrator-level permissions on their computer should not use the default "Destination Folder". Instead, use the 'Change' button to select a destination folder where you have write permissions [e.g., create a new folder in 'My Documents']. Similarly, administrators installing CDTree for other non-administrative users should install to a non-default "Destination Folder" in which the end user(s) can create/remove files and folders.

    ftp://ftp.ncbi.nih.gov/pub/mmdb/cdtree/Windows/CDTree.msi

  • Earlier Windows operating systems (or if the above links do not work):

    This is a larger download that contains an installation engine that can install the CDTree software on PCs that do not have a current version of the Windows Installer.

    ftp://ftp.ncbi.nih.gov/pub/mmdb/cdtree/Windows/CDTreeSetup.exe
     
  • Note for CDTree 3.0 users:
    You do not have to manually uninstall CDTree 3.0. The installation bundle for CDTree 3.1 will first uninstall all binaries installed by CDTree 3.0, including the original preview of Cn3D 4.2. Cn3D 4.3 will be installed by CDTree 3.1.


Depending on your computer's security settings, and those of your web browser, the installation bundle will either start automatically or it will be saved to your computer. You can explicitly save the installer bundle by right-clicking on its link and choosing 'Save Link As...' from the popup menu.

To run a saved installation bundle, simply double-click its icon.

The CDTree 3.1 installer has been configured to create the file and MIME type associations mentioned above. This enables the use of CDTree and Cn3D as helper applications to view and interact with any existing domain model or domain hierarchy defined in the Conserved Domain Database at NCBI. (See the PC test link below for an example.)

The CDTree 3.1 installer places the Cn3D executable consistent with CDTree's default setting for the path to Cn3D. If you later wish to move Cn3D, however, you must update the Cn3D path in the 'General' section of CDTree's Preferences tab to provide the new location. The updated CDTree preference setting must be applied and/or saved before it takes effect.

As a stand-alone command-line program, the fa2cd utility can be moved to any folder.

Uninstalling CDTree using 'Add or Remove Programs' from the Windows Control Panel removes the entire CDTree 3.1 distribution, including Cn3D 4.3. If you have the older Cn3D 4.1 on your computer, it will not be uninstalled during CDTree 3.1 uninstallation.
 
Test the PC Installation

You can test your CDTree 3.1 installation by clicking this link to download a project file from the CDD servers. CDTree should open on your screen displaying the RNR-PFL hierarchy with an appearance similar to the screenshot on the main CDTree page.

If a dialog similar to the following appears and you choose 'Save to Disk' you will need to double-click on the saved file (named 'cddsrv.cn4') to launch CDTree.

PC dialog for downloaded CDTree file from CDD



 
Mac Installation

CDTree 3.1 is supported as a Carbon application for Intel-based Macintosh computers running OSX 10.4 and higher; PowerPC Macs are no longer supported. To download the CDTree 3.1 software distribution, packaged as a zip archive, use the following link.

  • ftp://ftp.ncbi.nih.gov/pub/mmdb/cdtree/Mac/CDTree_intel.zip

  • Note:
    Mac OSX 10.3 onward provides a default zip archive file handler named either BOMArchiveHelper.app (10.3, 10.4) or ArchiveUtility.app (10.5). For earlier versions of Mac OSX, the freeware application Stuffit Expander is commonly used to extract files from archives. For more details, consult your computer's help documents, or review this short article.

Depending on which web browser you use and its preference settings, the downloaded zip files will either be unzipped automatically or it will be saved to your computer. You can explicitly save the installer bundle by Ctrl-clicking on its link and choosing 'Download Linked File As...' from the popup menu.

To unzip a saved file, simply double-click its icon. The contents of the archive are typically placed in a new folder contained in the same folder that contains the .zip file.

The CDTree.app and Cn3D.app application bundles are installed in the same folder, consistent with CDTree's default setting for the path to Cn3D. If you wish them to be in separate folders, simply edit the Cn3D path in the 'General' section of CDTree's Preferences tab to provide the new location of Cn3D.app. The updated CDTree preference setting must be applied and/or saved before it takes effect.

As a stand-alone command-line program, the fa2cd utility can be moved to any folder.

The downloaded application bundles have been configured with the file and MIME type associations mentioned above. This enables the use of CDTree and Cn3D as helper applications to view and interact with existing domain hierarchies defined in the Conserved Domain Database at NCBI.

 
Test the Mac Installation

You can test your CDTree 3.1 installation by clicking this link to download a project file (named 'cddsrv.cn4') from the CDD servers.

However, you need to provide a hint to Mac OSX the first time you run CDTree or Cn3D, either by downloading a file via the NCBI web site or by clicking on a saved project or conserved domain file. When asked, be sure to associate CDTree 3.1 with file type .cn4, and Cn3D 4.3 with file type .cn3. Similarly, the first time you receive a MIME message of a type from the table above select the appropriate application.

For example, Firefox presents a dialog similar to the following when clicking the test link. Of course, if you choose 'Save to Disk' you will then need to double-click on the saved file (named 'cddsrv.cn4') to launch CDTree.

Mac dialog for downloaded CDTree file from CDD in Firefox


Once those hints have been given, CDTree should open the downloaded project file on your screen displaying the RNR-PFL hierarchy with an appearance similar to the screenshot on the main CDTree page.

Note on web browsers:
Among the web browsers tested, Firefox and Opera both present a dialog that allows the user to choose an application with which to automatically open a downloaded file.  Safari always saved the downloaded file as 'cddsrv.cn4' into the folder specified in its 'Save downloaded files to:' General preference setting, and provides no means to automatically open that file.





Citing CDD: Marchler-Bauer A, Zheng C, Chitsaz F, Derbyshire MK, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Lu S, Marchler GH, Song JS, Thanki N, Yamashita RA, Zhang D, Bryant SH. CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res. 2013 Jan 1;41(D1):D348-52. 2012 Nov 28.   (Additional articles about NCBI's Conserved Domains Resources are accessible from the publications page.)

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