Contributed Software

Contributed software introduction by Tim Stevens — last modified 2006-12-12 13:39

Introduction to externally developed software distributed by CCPN.

How to deposit software by Wayne Boucher — last modified 2006-12-14 14:12

Instructions on how to deposit software.

Bruce D. Ray utility programs by Wayne Boucher — last modified 2006-12-12 13:43

1. Several rather simplistic utility programs to generate reports on assignments in 2D xeasy format peak lists. (Xeasy format used because of ease of coding for it. The reports generated vary in utility. This was originally done to evaluate assignments from garant 2.0) 2. A utility program to create a 2D xeasy format peaks list from the first four columns in a tab deliminited file. (Used in conjunction with the next program to convert Varian VNMR pks format 2D peak lists to xeasy format.) 3. A utility perl script to convert Varian (VNMR) pks format 2D peak lists to a tab delimited file. 4. A program for Varian (VNMR) 2D to Azara format conversion with parameters.

Graeme Ball Analysis macros by Wayne Boucher — last modified 2007-01-04 13:56

Extraction of data from experiments where a coupling is encoded as a splitting

Jeremy Craven utility programs by Wayne Boucher — last modified 2007-01-04 15:48

Command line utilites (mainly) for help in setting up NMR data acquisition.

Krystyna Bromek utility program by Wayne Boucher — last modified 2007-01-04 16:11

Command line utility (uses awk) for referencing NMR data and AZARA processing. Extracts spectrum description information from Bruker header files.

S Chandra Shekar NMRView scripts by Wayne Boucher — last modified 2007-01-04 16:28

Scripts to extract information, manipulate, or generate cross peak (.xpk) files in the 'nmrview' (an nmr data viewing, analysis graphical package by Bruce Johnson). Also contains the directory xpk2nv w/ Fortran77, C and Perl codes to simulate, from a given .xpk file, 2d/3d spectra in frequency domain by modelling the spectra as a collection of non-interacting Gaussian oscillators. The directory is grouped into subdirectories with mostly Perl scripts, with some c-shell, awk and a few sed scripts - there are about 225 in all. The usage information for almost all the scripts can be obtained just by typing the name of the script (change mode to executable, if that is a valid state; for e.g., c-shell and perl scripts can be made executable, but it is not meaningful to do so for awk and sed scripts). Bulk of the remainder of the scripts will have the usage information written in the code itself (so look at the source code near the top). NOTE: some of the scripts may use bmrb chemical shift information (so you may need to provide that table). there is such a file "bmrb.cs" in the main directory; but you may wanna use the latest updated table from bmrb (bioMagResBank). Also, if any of the scripts have the path to bmrb.cs hard-wired into them, you may have to edit it suitably.

Bob Diamond Clusterpose program by Wayne Boucher — last modified 2007-02-13 13:25

Clusterpose seeks families of similar structures within an ensemble of structures by repeatedly looking for the currently existing pair of clusters which may be superimposed on each other with a residual smaller than that for any other cluster-pair. Initially, each structure is a 'cluster' of 1. The resulting tree of combinations reveals groupings of similar structures. Alternatively, structures may be presented to Clusterpose in a sequence determined by the user, eg in energy order, and Clusterpose may be set to add these structures into a single cluster, one at a time, in the order given. This will show at what point the higher energy structures lose comparability with the low energy ones.