Resonance Assignment/Sparky

Sparky

INTRODUCTION

Sparky is a software package developed at the University of San Francisco for visualizing and analyzing multidimensional (2D, 3D or 4D) NMR spectra.  Sparky plays a critical role as the link between spectral data and assignment/structure determination programs.  The input for the program is processed spectra from various formats (NMRPipe, Felix, Varian or Bruker) converted into Sparky (i.e., “ucsf” format) via processing scripts supplied with the program.  One can output a variety of data from Sparky including:  chemical shift assignments, peak lists, and post script images of spectra.   In the following sections we describe the practical aspects of using Sparky and standard approaches employed by NESG researchers using this program in structure determination projects.  A descriptive on-line manual for a recent Sparky version (3.115) is available at: www.cgl.ucsf.edu/home/sparky/manual/index.html.

 

METHODS

1.  Conversion of processed spectra to Sparky input format

Typically we process NMR spectra using NMRPipe, hence it is necessary to convert the spectra from pipe to ucsf format using the following command:

          pipe2ucsf [options] filename.pipe filename.ucsf

For higher dimensional spectra a flag can be used to swap the dimension order if desired.  For example “-213” swaps the order of the 1st and 2nd indirect dimensions of a 3D spectrum.  This is applicable to many Varian 3D triple resonance spectra.
Another useful function is making 2D projections of higher dimensional spectra.  This is done using the “ucsfdata” command.  First, run the following command:

            ucsfdata filename.ucsf

to obtain a list of information for each dimension of the spectrum.  Then, for example, to make a 2D F23 projection of a 3D spectrum use:

            ucsfdata –s1 [# points] –r –o output.ucsf input.ucsf
        or
            ucsfdata –p1 –o output.ucsf input.ucsf

2.  Launching Sparky

To open a spectrum for the first time use:

            sparky filename.ucsf

To open a single save file or project (a collection of save files) use:

            sparky filename.save

            sparky filename.proj

If using Sparky for the first time, a Sparky folder will be automatically generated in your home directory, with various subfolders.  It is recommended that spectral (.ucsf), save and project files for a specific project be stored and launched from a specific directory in order to avoid confusion between multiple protein projects.  The .save and .proj files are simple text files which contain links pointing to where data (.ucsf and .save files) are located on your machine.  If a spectrum fails to open check the links in these files.
When Sparky is launched a menu box appears.  This box tracks all commands performed during a session.  One can make commands in Sparky using the mouse and clicking various commands under the different menus within the menu box or by using a plethora of two-letter “accelerators”.  A “pointer mode” box also opens at the start of a session and allows the user to toggle between various pointer modes.  Spectra are launched in individual windows.  See Figure 1.  All spectra are opened as 2D planes, with the additional dimension(s) of 3D and 4D spectra represented by sliders along the bottom of the spectral window.