The relaxation toolbox (ROTDIF)[1] has several important capabilities. First, it consists of a new version of the ROTDIF program[2,3], which can now simultaneously analyze relaxation data for 15N and 13C at several fields. The new ROTDIF 3.0 is orders of magnitude faster than the previous version, and is now able to accurately compute a fully anisotropic rotational diffusion tensor from a 250+ bond dataset in under 0.05 s, on a standard laptop. ROTDIF is also more robust, based on our simulations, when processing data with large conformational exchange contributions. Order parameters can also be rapidly computed. Finally, to improve accessibility to all the program features and simplify the user experience, we introduced a graphical user interface (GUI) that simplifies and speeds up the analysis of the data. The toolbox also contains ELM3 and ELMDOCK[5], a program for ab initio prediction of the rotational diffusion tensor from molecular structure, and the associated docking program that orients and docks a two-domain system based on relaxation data. The prediction can be computed in less than 0.1 s, and docking can be performed within a few seconds on a standard laptop.

1. Berlin, K., Longhini, A., Dayie, T. K., & Fushman, D., JBNMR 57 (2014) 333-352.

1. O. Walker, R. Varadan, D. Fushman, J. Magn Reson 168 (2004) 336–345.

2. N. Eldho, K. Dayie, J. Mol Biol 365 (2007) 930–944.

3. Y. Ryabov, D. Fushman, J. Am Chem Soc 129 (2007) 7894–7902.

4. K. Berlin, D. P. O’Leary, D. Fushman, Proteins: Structure, Function, and Bioinformatics 79 (2011) 2268–2281.

Instructions

1. Make sure Java 1.6 or higher is installed.
2. Download latest version from https://bitbucket.org/kberlin/armor/downloads
3. Unzip the file into a directory
4. Double click rotdif*.jar file, or alternatively, to run from command prompt, type "java -jar rotdif*.jar"

Note that * means wildcard insertion of the actual name.

Please cite reference [1] if you publish using this work.

ELMDOCK Settings

FAQ

Q. I get a library not found error. What should I do?

A. You need to download both, rotdif*.jar files, as well as the lib*.zip file. Create a ROTDIF directory and put the rotdif*.jar files into the directory. Then, unzip the lib*.zip files into the ROTDIF directory. The final ROTDIF directory structure should look like this:

./lib
./lib/***.jar  %all the jar files should be in the lib directory
./rotidf*.jar

Q. What is the format of the input file?

A. The input file is a white space delimited file. All the chain IDs and atom names must match the PDB file. The NOE data is optional, but significantly improves results. Use * to mark the specific residue as flexible, and use % to comment out a line. See example files and 2014 paper for more details.

<residue number> <chain id> <P atom name> <Q atom name> <freq of spectrometer (Hz)> <R1 rate (1/s)> <R1 error (1/s)> <R2 rate (1/s)> <R2 error (1/s)> <NOE> <NOE error>

A. How is the NOE defined?

A. I_sat/I_eq, where I_sat and I_eq are the signal intensities of nucleus P measured when the nucleus Q is in the saturated and in the equilibrium states, respectively.

Q. Can I run rotdif without a GUI interface, using a command line interface?

A. Yes. Use the "java -jar rotdif-1.1.jar -help" command.

The following options are available

Program flags: <program name> <flag> [<value>] <flag> [<value>]
ARMOR Version: 1.1, Build Time: 06/24/2014 12:49 PM
	Boolean flags do not contain a value key.
	Flag options are as follows:
		-axes, default = false
			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).
		-dock, default = false
			Perform docking of a two domain system and output rotation and translation.
		-elm, default = false
			Run ELM on the pdb file to predict data.
		-help, default = true
			Displays the help menu.
		-model, default = 1
			Model number of the pdb file.
		-nodynamics, default = false
			Do not compute dynamics, only tensor (speeds up computation).
		-nogui, default = false
			Use commandline, instead of GUI, interface.
		-nostat, default = false
			Do not compute statistics (speeds up computation).
		-out, default = ""
			Root string for the names of output PDB files and axes, if requested. Not generated if set to empty.
		-pdb, default = ""
			Name of the PDB file to use for calculations.
		-relax, default = ""
			Name of the relaxation file to use, ROTDIF format.
		-robust, default = false
			Perform robust least-squares regression (outlier suppression) were possible.
		-temp, default = 298.0
			Temperature for relaxation in Kelvin.