Small Angle X-ray Group Home page
The following programs developped in our group can be downloaded free of
charge for academic purposes. Please click each program name, and input your
information. You can obtain the program as informed by E-mail.
- SAXS_MD 1.15 |
Restrained molecular dynamics (MD) with SAXS constraints. All the source
codes, manual, and some utility programs are available as a single package.
The package does not contain a program to carry out MD itself, and the
program can be used in combination with various MD packages.
In version 1.15, calculation in dimensionless scale is possible in order to
consider the effect of hydration shell.
- SaxsMDView 0.92 |
Molecular graphics program to visualize molecular structure along with
constraint force vectors calculated by SAXS_MD. Source code, manual, and
example files are available as an archived file. The program requires OSF
Motif and OpenGL environments in its installation and run. For detailed
information, please see J. Synchrotron Radiat. 15, 535-537 (2008).
Programs for tracing beads in the in the beads-ensemble structure such
as that obtained with GASBOR. The programs solve this problem in terms of
Graph Theory by finding a Hamilton path, regarding the beads and their
neighbouring connections as vertices and edges, respectively. The package
contains two programs, MakeEdge and Hamilton-path. MakeEdge lists all the
neihbouring connections inside the bead-ensemble structure as 'edge'.
Hamilton-path program searches for the Hamilton path to pass over all the
beads exactly once by tracing the edges. The former program is written in
Fortran, and the latter in Scheme, a dialect of Lisp.
SAXSANA program was developed by Dr. Hiragi's group at Kyoto University.
It is an interactive analytical program for SAXS measurements to provide
various tools for the data treatment and analyses. The program supports
data format of BL10C and BL15A of Photon Factory in KEK, but the free format
is also available. For more detailed information, please see J. Synchrotron
Radiat. 10, 193-196 (2003) . SAXSANA was written with Microsoft Visual Basic 5.0
and runs on Windows platforms. The package contains all the source codes,
setup.exe, and sample data, and is distributed on this server under the
- SaxsAnalysis |
Program package for analysis of SAXS data such as Guinier, Porod/Luzzati,
and Zimm plots and p(r) calculation. Anarg32n, Porod32n, Zimm32n programs
are QuickWin applications running on Microsoft Windows, and Saxfft3n runs on
N88-BASIC environment/emulator. The manual document is only for Japanese.
This program package is originally intended to use in data treatment at
BL15A of Photon Factory in KEK.
In case of data measured with PSPC, please use PSPC-version.
- SVD & Reconstruction |
A powerful tool for analyzing polydisperse system. SVD (Singular Value
Decomposition) estimates the number of independent components in the system.
Based on the equilibrium (static) or kinetic model, intrinsic SAXS profile
in each component can be reconstructed. Two- or three-state (sequential)
transition model is supported in static or kinetic analysis. Main routine of
SVD is based on the algorithm in Numerical Recipes in Fortran (Cambridge
Univ. Press). Althogh the package is originally intended to analyze static
or kinetic SAXS data for protein unfolding, it may be also applicable to
other experimental method such as CD, or other static/kinetic process
accompanying conformational changes.
Bioinformatics Laboratory, Tokyo University of Pharmacy and Life Sciences