This archive contains the files:
- gnom_Dmax_scan.pl
- eval_GNOM_transform.m
- check_Ireg_Pr.m
- dammin_reconstruction_series.pl
- damaver_series_average.pl

The files ending in .pl are perl scripts,
the files ending in .m matlab scripts.

Together, these scripts can be used to obtain low resolution
structure models from small-angle X-ray scattering (SAXS) data.
They use several programs by the Svergun group:
GNOM, DAMMIN, DAMAVER, and SUPCOMB.
Executables of these programs as well as their documentation 
can be obtained at:
http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html


Each of these scripts is documented in a header preceeding the 
program. The headers can be viewed by opening the files with 
any text viewer.

The typical usage follows the following general outline:
1. Start with a background subtracted SAXS profile.

2. Use the script gnom_Dmax_scan.pl to run the program 
GNOM with different values for the parameter Dmax
(the maximum intramoleculat distance) to obtain real space
distribution functions P(r) (the distribution of pairwise distances). 

3. Evaluate the P(r) solutions for different Dmax values using the matlab
scripts eval_GNOM_transform.m and check_Ireg_Pr.m and determine 
an appropriate value for the parameter Dmax.

4. Run a series of ab inito shape reconstructions (typically similar to 10)
using the script dammin_reconstruction_series.pl
This script uses the output files of the GNOM runs as inputs
and outputs PDB files for each generated model.

5. The models generated in the previous step can be compared and averaged
using the script damaver_series_average.pl.
 
If you find these scripts useful,
please cite them as: -------------------------------------------------------
Jan Lipfert, Rhiju Das, Vincent B. Chu, Madhuri Kudaravalli, Nathan Boyd, 
Daniel Herschlag, and Sebastian Doniach   
"Structural Transitions and Thermodynamics of a Glycine-Dependent 
Riboswitch from Vibrio cholerae", J. Mol. Biol. 365:1393-1406 (2007)
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If you have any questions, please email
Sebastian Doniach (doniach@drizzle.stanford.edu)
or
Jan Lipfert (j.lipfert@tudelft.nl)