Setting up Sparky project

From NMR Wiki

Setting up a project helps analyzing data sets containing multiple spectra and helps avoid opening all spectra over and over and remember all user settings customized in the previous sessions.

Sparky project concepts

Sparky has a bug in saving paths to binary data files inside .save files and paths to .save files inside the .proj file. To correct the problem one can open those files in the text editor and substitute relative paths with the absolute ones (starting with / in Unix and with the drive letter in Windows)

Sparky project consists of a collection of files.

Binary NMR spectrum data (.ucsf and processed bruker files). Source spectrum data files in the native sparky format have .ucsf extension (sparky can also directly read processed Bruker data - 2rr files and probably 3rrr files). This tutorial assumes that you already have .ucsf files.

Spectrum meta-data files (.save). In the project, each binary spectrum data file has an associate file with .save extension. This file contains plain text and can be edited by any text editor. This .save file contains additional data pertaining to the binary file: contour drawing settings, positions of picked peaks, labels, etc.

Main project file (.proj). This file contains links to .save files and additional project meta-data: resonance positions, user options and more. Main project file usually has .proj extension. All information in .proj file is stored in plain text format

Setup instructions

First start Sparky. Then open each .ucsf or Bruker processed data file, then create .save files by first selecting the spectrum display window by clicking anywhere inside of it and then selecting Save as... command in file menu. If you already have a project set up and you want to include another spectrum - first open the project, then follow above steps (you will still need to save the updated project as described below).

Perhaps a little confusing part of sparky is that there are two Save As... menu items. You should select the upper one for .save files and the second Save As... for the .proj file.

If you don't want to save files in the Sparky default directory, then you will have to navigate to desired location in the "Save spectrum dialog".

You can set the SPARKYHOME environment variable before you start sparky to the directory that contains your Save, Project and Lists directories. Sparky will by default open and save files at that location. If the Save, Projects and Lists directories are not yet present a popup will ask whether you want to create then.

For example if you use the bash shell:

cd /home/gaga/nmr/myprotein/Sparky
export SPARKYHOME=/home/gaga/nmr/myprotein/Sparky
sparky &

Finally, create the .proj file by selecting the project Save As... item in the "File" menu.

In case you did not choose default directories for the file location (which makes perfect sense if you are working on several projects) - then you will have to do some extra work - due to a bug (and the workaround) described in the section above.

In addition you might want to create suitable name labels for the spectra that are displayed in the "Windows" menu.