1. How can “PINE2SPARKY” converter imply many probabilities from PINE?

PINE does not provide absolute assignments for each peak. It provides possible assignments including the probability that the assignment is correct because PINE uses a probabilistic approach. Multiple possible assignments are converted into labeled objects and the labeled objects are incorporated into SPARKY save files. Since a peak cannot attached to several labels at once in SPARKY, the labels should include position information. The information is saved not only in SPARKY save files but also in newly created files with names that have “_pl” at the tail of the save files because labels are temporary so they can be changed later.

The format of the labels is similar to the following:

possible assignments[probability]:(peak positions)

ex) A14CA-A14N-A14H[0.988]:(60.342,120.231,7.764)

There can be many labels for one peak and once the user determines which assignment is correct, the incorrect labels can be removed. The probable ranks are color coded such that in the default settings, blue labels show the best probability. You can change the color in the PINE2SPARKY program.

 2. User Interface

- New PINE2SPARKY converter
New PINE2SPARKY converter provides much easier user interface for setting input and output files.
You can just follow step-by-step instructions.

1) PINE outputs- step 1

2) SPARKY inputs- step 2

3) Ornaments and Tolerances- step 3

4) SPARKY outputs- step 4

- Old PINE2SPARKY converter (only for MacOSX Tiger)

The user interface of old PINE2SPARKY (only for MacOSX Tiger) consists of roughly four parts: 1) SPARKY inputs, 2) PINE outputs, 3) Sparky outputs, and 4) controls.

PINE2SPARKY converter

1) Sparky inputs

To set the spectra identifier, prepare a peak picked SPARKY project and open it here by pressing “Browse...” button. The save files will be automatically listed in the PINE2SPARKY. If you want to change it, you can press “Browse...” button separately to reset.

2) PINE outputs

You will need a protein sequence file and at least one of the native PINE probabilistic output files. The sequence file can use either the three or one character amino code.

3) Sparky outputs

SPARKY output files are automatically set when you set SPARKY input files. Therefore, performing this program will automatically overwrite your original files. If you do not want to make copies of the original files, you can change the file names by pressing “Browse...” buttons.

4) Controls

(1) Preferences

You can change the default preferences to your own setting. The default for the first index of the sequences is set to 1 and tolerances are set to 0.4, 0.4 and 0.03 for C, N and H-respectively.

(2) Spectrum identifier

PINE2SPARKY generates artificial spin systems for each spectrum and matches these with picked peaks in the SPARKY inputs. So PINE2SPARKY must know spectrum types for SPARKY save files in order to generate proper artificial spin systems. The identifier is used to search for the unique file name in the save files.

(3) Options

The color of the labels for one peak is determined by the ranks of the probabilities. In the default settings, blue is set to represent the highest probability and purple is the next highest. If you want to change colors for ranks, press the “Option...” button and change them.


After setting up everything you must do, probable assignments from PINE are converted into PINE labels in the Sparky save files by pressing “PINE2SPARKY” button. In addition, “_pl” files which have PINE label information are generated. PINE labels in Sparky save files are not eternal since one can change the position of the labels or remove them entirely, therefore the PINE results should be moved into a permanent file. The time it takes to convert a file is dependent on how many peaks exist in your project.

 3. Usage