In-house software

A number of useful in-house programs have been produced that are available for download. Programs are either in C++ (making frequent use of the GSL), python (2.7, usually requiring numpy, scipy, matplotlib and nmrGlue modules) or a mixture of both. Outputs are produced in either gnuplot, matplotlib or latex. For programs with graphical user interfaces, wx-python will be required. Specific installation instructions and requirements are described for each program individually.

All have had testing on mac, linux and windows, on both 32 and 64bit chipsets.

Please get in touch if you have any problems with installing and using these guys!

[PLEASE NOTE: Download links are not setup yet! work in progress...]

1. Sign determination by R

Python code to help with the determination of signs of chemical shift differences using the R method. The code takes a pb, kex and a list of chemical shift differences, and determines optimal B1 fields and offsets from numerically evolving the appropriate Louvillian. Effects of differences in transverse relaxation between exciting both upfield and downfield of the resonance of interest are calculated. Varian input macros files are produced, so that you only need type ‘go’ at the spectrometer. The program uses nmrPipe and nmrGlue to process data and will also analyze everything for you. Signs made simple!

Measurement of the signs of methyl chemical shift differences between ground and excited protein states by R: an application to αB-crystallin
Baldwin AJ, Kay LE
J. Biol. NMR (2012) 53(1) 1 pdf

2. Polymake

Python code for taking a pdb ‘building block’ file and assembling it into a polyhedra. Modelling restraints, such as enforcing a minimum distances between two points are implemented. Modified fortran code is provided for rapidly calculating PA collision cross section values, to enable models to be compared to experimental collision cross section data.

The polydispersity of αB-crystallin is rationalised by an interconverting polyhedral architecture
Baldwin AJ, Lioe H, Hilton GR, Baker LA, Rubinstein JL, Kay LE, Benesch JLP
Structure (2011), 19, 1855-63

3. Champ

Used to analyze 1D electrospray mass spectra where a protein M is binding a ligand P giving complexes with stoichiometries of the form MiPj. The program assumes that the concentrations of the various complexes can be described by a continuous distribution function. We applied this approach in studies of clients binding to sHSP oligomers.

Dissecting heterogeneous molecular chaperone complexes using a mass spectrum deconvolution approach

Stengel F, Baldwin AJ, Bush MF, Hilton GR, Lioe H, Basha E, Jaya N, Vierling E, Benesch JLP
Chem & Biol. (2012), 19, 599-607
commentary Slingsby C, Clark AR

4. Champion

Used to analyse batch 2D electrospray/ion mobility data. Details to come.