Chapter 4. More Details on Features

Table of Contents

Janocchio Files
Creating, saving and opening files
NOE Calculation Parameters
Equivalent Protons
Coupling Constant Calculation Parameters
Vicinal Proton-Proton
Vicinal Proton-Carbon
Cell Colouring
Obtaining 3D structures

Janocchio Files

1. Structure files

In principle, Janocchio can understand all structural file types supported by the underlying Jmol program. Tested file types for single structures are mol, sdf or xyz, and for multi-structure files, sdf and xyz files. Structure files are loaded via File -> Open.

2. Janocchio NMR data files

This is own file format (extension .jsn): it stores all information you enter within the Janocchio program, including atom labels, defined NOEs and coupling constants, experimental values, conditional formatting, NOE and coupling parameter settings, and NAMFIS populations. It does not store the structure or structures itself, but it does remember which structure file was used with this data. Thus if you try to apply an NMR data file to the wrong structure you will be warned (but not stopped).If no structure is loaded and you load an NMR file, you will be asked if you want to load the structure. NMR data file are loaded via File -> Read NMR Data.

If you are using NAMFIS as an applet, navigating away from the web page will save a '.last.jsn' file. On reloading the web page, the applet will ask if you want to restore this.

3. NAMFIS output files

Janocchio can read NAMFIS output files and apply the population information contained therein to the currently loaded structure set.

Creating, saving and opening files

Typically, for a new problem, the user would start by loading a structure file with File->Open. Next he/she would calculate NOEs and couplings with Janocchio, then save an NMR data file with the results (File -> Save NMR data).

To return to this data at a later point, the user can simply load the NMR data file (File -> Read NMR data). The user will be prompted to load the associated structure.

If you want someone else to view the Janocchio results, give them both the structure file and the Janocchio NMR data file: remember, the structure is not stored in the NMR data file, only a reference to it. The second user would nead to load the structure (File -> Open), then the NMR data file (File -> Read NMR data).