Software and Pulse Programs

CDSSTR - Secondary Structure from Circular Dichroism Spectra

This program is a Python wrapper to W. Curtis Johnson's original CDSSTR program, available here. The core program is identical to Dr. Johnson's, but our version has been augmented with several features to make analysis simpler. As a result, it's often possible to perform the analysis without having to edit a single text file. New features include:

  • Automatic conversion between molar extinction and mean residue ellipticity
  • Automatic adjustment of the basis set when wavelength limits are less than 260 and more than 178 nm
  • Streamlined spectral entry with simple consistency checks
  • Multiplatform support (currently Windows and Linux, requires Python 2)
  • Command line and windowed interface available (requires Tkinter)

Note that the binaries are encoded in to the python code itself; you do not have to download anything else. Additionally, the Fortran source code is in the file itself (extract it using the -C parameter). This source code can be compiled using gfortran, and the resulting binary can be used if Linux or Windows platforms aren't readily available.

Download: (228 K)

SOLEXSY-GUI- GUI Interface for Solvent Exchange Spectroscopy Fitting

This is a MATLAB program for fitting hydrogen exchange profiles from the SOLEXSY pulse program (originally published by Dr. Nikolai Skrynnikov's lab). The original paper is available here. This version of the software contains all of the original "guts" of the fitting routine -- the solver uses the same original code to determine kex -- but a GUI interface is implemented to make fitting easier. Additionally, the input was modified to take a peak list directly from Sparky instead of NMRPipe's autoFit routines. In our experience, using the Sparky list is much more intuitive and produces identical results.

The program runs in any version of MATLAB, and further instructions are given in the "Read Me" file.

Download: solexsy.tar.gz (43 K)

xmgrace Unit Conversion Worksheet

xmgrace is a popular software package used by our lab to generate publication-quality figures. Unfortunately, the units used by this software for font size, line thickness, etc. are somewhat arbitrary and depend on the smallest dimension of the plotting workspace. This worksheet lets the user easily determine the Grace font sizes and line widths that correspond to common standards set by journal publishers. The associated Default.agr file (to be placed in ~/.grace/templates/) uses appropriate values for an 8 cm wide figure.