Useful Software and Scripts

(Sorted alphabetically)


This is a script to run the 2ptrate calculation as needed for the rcCPMG experiments. From the Loria Lab.


A script adding lines of zeros to a file containing residue gaps. Useful for comparing data of partly assigned mutants that were pasted in the same text file side by side. To avoid residue gaps, run add_0 on the individual mutants and then paste the individual mutant data together in a single file. From the Gagné Lab.

CPMG Scripts

A collection of essential scripts for rcCPMG processing. This compressed file includes,,, dispplot, and allpdf8. Note that CurveFit is essential for processing the CPMG scripts and that the allpdf8 macro requires the ghostscript and psutils linux packages. From the Loria Lab.


A default .cshrc file edited according to our typical usage.


A general fitting program designed for batch use. Essential for processing the CPMG scripts. Note that recent linux distributions (e.g. Ubuntu 11.10 and up) may require recompiling the program from the source code, which is available upon request. Instructions: install the gfortran compiler, untar source code, type 'gfortran -c *.f', type 'make', transfer the recompiled program folder to /usr/local. Enjoy fitting data! From the Palmer Lab.

FAST ModelFree

A Perl program to assist in the analysis of laboratory frame spin relaxation data. It interfaces with ModelFree and fully automates the process of model selection and tensor optimization. From the Loria Lab.


A GUI to produce a multipage PDF on linux. Very simple and efficient.


Kaiser window function for nitrogen processing. Usually in /usr/local/nmrPipe/nmrtxt/.


A software tool for simulation of NMR line shapes from HSQC titration series and ITC profiles in multi-state systems. From Evgenii Kovrigin.


A very good software to organize your research paper collection and citations. An excellent alternative to the Mac software Papers, Mendeley can be installed on all platforms. Best of all: it's free!


A program for optimizing "Lipari-Szabo model free" parameters to heteronuclear relaxation data (ps-ns dynamics). A FORTRAN 77 compiler is required to compile the ModelFree source code. In addition, you will need the BLAS and LAPACK libraries installed. Xmgrace is also required. From the Palmer Lab.


Essential software for processing, analyzing, and exploiting NMR spectroscopic data. This suite also includes nmrDraw. Make sure you are in the C-shell (tcsh) and that all the dependencies are resolved prior to installation. See instructions. On 64-bit workstations, you need to install 32-bit libraries first. On Ubuntu linux : sudo apt-get install ia32-libs

A standard for NMR data processing.


PyMol is the most powerful molecular visualization program out there and by far the best one to create images for publication. You can also download a couple of scripts that I collected and modified over the years for publication purposes (PDBs and maps are also included). I've included 3 that were used to create some of our paper figures. Many more are available upon request.


Evgenii Kovrigin's Python library. It interfaces with Sparky and it is essential for running the CPMG scripts. Installation instructions.


relax is a software package designed for the study of molecular dynamics through the analysis of experimental NMR data. It is a very powerful alternative to the model-free analysis of protein dynamics.

Simple Linux Backup Software

No further explanation needed. Very user friendly.


A graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers. Installation instructions.


Sparky2rate is a Perl script that will process the output from the Sparky command "rh" using the rigourous statistical analysis afforded by the program Curvefit. This is a newer version that works with the updated version of Curvefit. From the Loria Lab.

SSH Tunnel

To make an SSH tunnel from a terminal: ssh -fND localhost:15555 username@worstation.ip.address. Then in Firefox: Preferences--Connection--Settings--Manual Proxy Configuration--SOCKS host: localhost--Port: 15555.


A script to run the statistical analysis of data columns (average, max value, min value, sandard deviation, etc.). From the Gagné Lab.