Xipp

(v 1.17.11)

(Created November 2017)



Purpose /Background

Xipp (pronounced zip) is an NMR analysis software package created and supported by Dr. Daniel S. Garrett in the lab of Dr. G. Marius Clore. This software package is designed to study labeled proteins and nucleotides and is a complete re-write and extension of the PIPP package using Java. Xipp uses the same file format for Peak-Pick files and assignment tables as was used in PIPP. In addition many of the keyboard and mouse commands are the same as used by PIPP. The primary differences between PIPP and Xipp is that Xipp allows multiple NMR experiments to be viewed and overlayed at same and has built-in ability to aid in backbone assignment. The most important difference is that PIPP is no longer supported while Xipp is actively supported.

Xipp groups related NMR experiments in a Study such as:

Backbone Assign

Sidechain Assign

Noesy Assign

Fast Exchange

Experiment Series (typically series of 2D 15N-HSQC spectra)

Generic Series (plots/tabulates intensities)

Two-Point & MultiPoint Rate (T1, T2 & T1p)

Two-Point & MultiPoint PRE

Two-Point & MultiPoint Delta Rate

CPMG Dispersion

JHN RDC ARTSY







Documentation

The PDF files shown below are also installed with the Software Package under v1/Documentation.

Documents

createSetStudies

Describes how to start Xipp under Linux and MacOS and describes how to create and set the properties for every type of Study. The properties for each Study are saved in *.xipp files.

Xipp_Commands

Describes the menus, tool-bars, dialogs, commands and buttons in Xipp.

backboneAssignStudy

Describes in the form of a tutorial using Xipp to make backbone assignments with the 85 residue protein HPr.





Download / Install Latest Versions

The software is developed and initially tested under Linux and as such performs best under the Linux OS. At this time only Linux and MacOS computers are supported. Windows support is planned but not guaranteed. The packages below were created using Install4J and install easily on every system tested.

General Installation Instructions

Download and install the Software Package first for your computer type. The Software Package must be installed first and contains the Java classes, source code and Jython library to run Xipp under any system that supports Java. Included is the Java runtime for the OS and a single 15N HSQC example. Detailed install instructions for each OS are listed below.

Accept all defaults when installing the Software and Example Data Packages until you are familiar with the software and know what you are doing. The Software package expects the Example Data Package to be installed in the same directory as the Software Package and the Examples will not work if the Example Data are put into a different directory than the Software. The default directory is ~/Xipp which is created when Xipp is installed.

The Example Data Package labeled *_ALL3D.sh includes all of the Example data excluding 4D data. The *_ALL3D.sh Example Data Package is a large file and will take more than 5 minutes to download. The separate Example Packages for individual Studies exist in order to download smaller images. If you install the Exmpl_*_ALL3D.sh package you only need to install the Exmpl_*_NOE4D.sh to have all of the examples.

Each user must install their own copy of the Software and Example Data. There is no network install option.

Linux

To install the Software and Example Packages under Linux open a terminal and run the package. You will most likely have to make the package executable with the chmod +x command. The packages are executable shell scripts under Linux/Unix. This will start the Install4J installer.

Must install the Software Package before the Example data Packages.

Software Package

xipp_Linux_1_17_11.sh (54 MB)

Example Data Packages

Exmpl_Linux_ALL3D.sh (686 MB)

Exmpl_Linux_Artsy.sh (24 MB)

Exmpl_Linux_Backbone.sh (121 MB)

Exmpl_Linux_HCCH.sh (120 MB)

Exmpl_Linux_NOE3D.sh (291 MB)

Exmpl_Linux_Relaxation.sh (131 MB)

Exmpl_Linux_Titration.sh (6 MB)

Exmpl_Linux_NOE4D.sh (1.9 GB)

MacOS X

To install the Software and Example Packages under Mac double click the downloaded file which is a Mac Disk Image file. This will open a new finder with a single entry. In the new finder window is an entry labeled xipp Installer for the Software Package. Hold the Control Key down while clicking the “xipp Installer” and select Open in the popup menu. This is required because from Apples point of view I am an unidentified developer. Click Open in the warning dialog to start the Install4J install process. The *_Pre_Lion Software package should be used on MacOS Versions 10.5 Leopard and 10.6 Snow Leopard. In MacOS Version 10.7 Lion and later the Java runtime became unbundled from the MacOS so it has to be installed with the software.

Must install the Software Package before the Example Data Packages.

Software Packages

xipp_macos_1_17_11.dmg (55 MB)

xipp_macos_1_17_11_Pre_Lion.dmg (27 MB)

Example Data Packages

Exmpl_Mac_ALL3D.dmg (691 MB)

Exmpl_Mac_Artsy.dmg (29 MB)

Exmpl_Mac_Backbone.dmg (125 MB)

Exmpl_Mac_HCCH.dmg (125 MB)

Exmpl_Mac_NOE3D.dmg (296 MB)

Exmpl_Mac_Relaxation.dmg (136 MB)

Exmpl_Mac_Titration.dmg (11 MB)

Exmpl_Mac_NOE4D.dmg (1.9 GB)



Previous Versions

Version 1.14.10 (Created October 2014)