PATI (Prediction of Alignment Tensor through Integration) Toolbox

The residual dipolar coupling (RDC) toolbox is similar in concept to the relaxation toolbox, and also consists of two main components. First, it contains a program that can compute molecular alignment tensor from 15N and/or 13C residual dipolar couplings. Second, it contains PATI (1) program that can quickly predict alignment tensor based on molecular shape for planar, steric alignment media. The prediction can be done in less than 0.1 s. This prediction algorithm is used in PATIDOCK (2) to rapidly (within a few seconds) align and dock a two-domain system based on its overall alignment tensor.

1. K. Berlin, D.P. O’Leary, D. Fushman, J. Magn Reson 201 (2009) 25–33.

2. K. Berlin, D.P. O’Leary, D. Fushman, J. Am Chem Soc 132 (2010) 8961–8972.

Instructions on using PATI:

1. Make sure you have Java 1.6+ installed
2. Unzip PATI into a directory
3. Open command prompt (in Windows go to start/run and type "cmd")
4. Switch into the directory where PATI is unzipped
5. type java -jar pati-1.0.jar -help, help should appear.

Example

java -jar pati-1.0.jar -rdc "rdcdata.txt" -pdb 1d3z.pdb -draw -bicelle 0.04

Options

To get help type java -jar pati-1.0.jar -help The following options are available:

Program flags: <program name> <flag> [<value>] <flag> [<value>]
ARMOR Version: 1.1, Build Time: 06/24/2014 12:53 PM
	Boolean flags do not contain a value key.
	Flag options are as follows:
		-axes, default = ""
			Name of the PyMOL script file for tensor axes. Not generated if set to empty.
		-axesl, default = 5.0
			Length of PyMOL axes extension beyond the molecule bounds (in Angstroms).
		-bicelle, default = 0.03
			Bicelle volume fraction.
		-dock, default = false
			Perform docking of a two domain system and output rotation and translation.
		-dockpdb, default = ""
			Name of the output PDB file used for Patidock. Not generated if set to empty.
		-draw, default = false
			Draw the fit plots.
		-help, default = false
			Displays the help menu.
		-model, default = 1
			Model number of the pdb file.
		-nostat, default = false
			Do not compute statistics (speeds up computation).
		-pdb, *required, 
			Name of the PDB file to use for calculations.
		-rdc, default = ""
			Name of the RDC file to use for calculations. CNS or PATI format.
		-robust, default = false
			Perform robust least-squares regression (outlier suppression) were possible.