I. Introduction

 1. What is the “PINE”?

PINE is a program that uses the sequence of a protein in conjunction with peak lists (or spin systems) from a variety of NMR experiments to generate the following: 1) automatic backbone and sidechain assignments, 2) detection and automated correction of potential referencing problems or inconsistent assignments, and 3) secondary structure determination.

PINE Server

- http://miranda.nmrfam.wisc.edu/PINE/

 2. What is the “SPARKY” and its extensions?

Sparky is a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers.


The software is free and can be downloaded at:

- http://www.cgl.ucsf.edu/home/sparky/

Using the PYTHON language, you can write extensions - small programs that access peak and spectrum data and use the display capabilities of Sparky. This capablity is included with the Sparky distributions after 3.106. Python web site http://www.python.org.

SPARKY extensions


 3. What is the goal of this project?

Using an unassigned peak list from SPARKY, our PINE server provides assignments for each peak along with the probability that the assignment is correct. Since the PINE server provides multiple possible assignments for one peak, users should choose one of them and confirm the assignment using SPARKY. We chose SPARKY as the assignment software because it is very popular for assigning spectra in the NMR community due to its ease of use and many features for visualizing spectra.

To make the PINE outputs work in SPARKY, we did following:

1) Developed a converter for PINE outputs to work as SPARKY inputs. The converter allows multiple PINE assignments for each peak to be input into SPARKY.

2) Developed SPARKY PYTHON extensions for manipulating and visualizing the information from PINE.

 4. System Requirements

Supported OS: MS-Windows, MacOSX, Linux 32bits and 64bits.

The PINE2SPARKY converter is written in Lazarus (which is an IDE of Free Pascal and a compiler that works in multiple operating systems). The SPARKY extensions are written in PYTHON which also works on multiple operating systems.

 5. Installation steps (Download)

We provide both source files and binary files. It can be downloaded from NMRFAM Software Download Page. However, for your convenience, NMRFAM Sparky Distribution already integrated PINE-SPARKY inside with other useful tools. If you want to install only PINE-SPARKY on top of your pre-installed SPARKY, follow instructions below.


Installation from source codes

Installation from binary

2) PYTHON extensions