How to obtain chemical shift reference offsets with PANAV

1. PANAV-the reference tool

The backbone chemical shift data can be used in the molecular fragment selection for CS-Rosetta structure prediction protocol. Successful use of chemical shift for secondary structure inference requires the correct referencing. PANAV (Probabilistic Approach to NMR Assignment and Validation) is a Java based structure-independent chemical shift validation and re-referencing tool. It is based on using residue-specific and secondary structure-specific chemical shift distributions calculated over small (3-6 residue) fragments to identify mis-assigned resonances. This application can be dowloaded from following link:

2. Compile the applicaiton

JAVA ( ) is requried for this programe.

mkdir ~/java
cp ~/java
cd ~/java
cd PANAV/standalone
javac *java

3. Run PANAV

 cd ~/java/PANAV
java standalone.PANAV

Then you will see a GUI like follow

click File, select Read .str File and then browse to a bmrb file.
The programme will process the data automatically. A few seconds later, you will see the result

The detected reference offsets are: CO: 0.00ppm CA: -0.10ppm CB: 0.25ppm N: 0.72ppm