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Analytical Ultracentrifugation - SEDFIT

SEDFIT is a data analysis software for sedimentation velocity, sedimentation equilibrium, and dynamic light scattering.

Instructions on SEDFIT Download

System requirements

• PC with at least 500 MHz, 256 MB RAM, Pentium or Xeon processor (Cyrix 3 processors may not work)
• Windows NT, 95, 98, XP, 2000 or later
• ~1.5 MB of hard disk space
• Internet connection for accessing this on-line help system

(We do not recommended use of the data acquisition computers XL-A or XL-I for data analysis with SEDFIT except when using the real-time mode.)

Installation

1) Note that this is software was created at the National Institutes of Health and carries the following disclaimer:

THIS SOFTWARE IS PROVIDED AS IS, AND WITH ALL FAULTS. THERE ARE NO WARRANTIES OF ANY KIND, EXPRESS, IMPLIED OR STATUTORY (INCLUDING, WITHOUT LIMITATION, TIMELINESS, TRUTHFULNESS, SEQUENCE, COMPLETENESS, ACCURACY, FREEDOM FROM INTERRUPTION). THERE ARE NO IMPLIED WARRANTIES ARISING FROM TRADE USAGE, COURSE OF DEALING, OR COURSE OF PERFORMANCE, OR THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. THERE IS NO WARRANTY THAT ANY SOFTWARE, INFORMATION, OR OUR EFFORTS WILL FULFILL ANY OF THE USERS PARTICULAR NEEDS OR PURPOSES

Please cite the software in publications and reference the method used.

2) Create a directory named "SEDFIT" on your computer's C: hard drive.

3) SEDFIT consists only of an executable sedfit.exe (NOTE: the older help file, sfhelp.hlp, is obsolete and not distributed anymore). Download the program file by simply clicking on the following link and store the file in the new SEDFIT directory.

sedfit93.exe (1180kb, this is the newest version 9.3b from 03/13, see information on the latest changes)

For help: Only the online-help system is supported at this time. It has the advantage that it can be kept up-to-date easily.

4) If it doesn't exist already, create a directory named "windows" on your C: hard drive. This directory will contain some configuration files once SEDFIT is running.

Double-click on SEDFIT, and the SEDFIT window should open. The first time you start the software, a prompt will appear to accept the disclaimer. After these steps, the program is ready to be used. If you are not familiar with the software, be sure to read about Getting Started.

5) If you would like to be placed on an email list of users for updates, bug fixes, etc., please send an email to:

schuckp@mail.nih.gov  with subject line: SEDFIT USER LIST

Resources

The approaches implemented in the software are described in detail in publications below.

• Dam J and Schuck P. Calculating sedimentation coefficient distributions by direct modeling of sedimentation velocity concentration profiles. Methods in Enzymology 384:185-212, 2004. [comprehensive review of the concepts and numerical methods]
• Schuck P. On the analysis of protein self-association by sedimentation velocity analytical ultracentrifugation. Analytical Biochemistry 320:104-124, 2003. 
• Schuck P. A model for sedimentation in inhomogeneous media. I. Dynamic density gradients from sedimenting co-solutes. Biophysical Chemistry 108:187-200, 2003. 
• Schuck P. A model for sedimentation in inhomogeneous media. II. Compressibility of aqueous and organic solvents. Biophysical Chemistry 108:201-214, 2003.
• Schuck P, Perugini MS, Gonzales NR, Howlett GJ and Schubert D. Size-distribution analysis of proteins by analytical ultracentrifugation: strategies and application to model systems. Biophysical Journal 82:1096-1111, 2002. [non-linear regression of c(s) and comparison with other methods, extrapolation of ls-g*(s) to infinite time]
• Solovyova A, Schuck P, Costenaro L and Ebel C. Non-ideality by sedimentation velocity of halophilic malate dehydrogenase in complex solvents. Biophysical Journal 81:1868-1880, 2001. [concentration-dependent sedimentation]
• Schuck P and Rossmanith P. Determination of the sedimentation coefficient distribution g*(s) by least-squares boundary modeling. Biopolymers 54:328-341, 2000. [analysis of g*(s) and introduction of the ls-g*(s) method without Dt-broadening]
• Schuck P. Size distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and Lamm equation modeling. Biophysical Journal 78:1606-1619, 2000. [continuous size-distribution analysis c(s) and c(M) with Tikhonov-Phillips and maximum entropy regularization]
• Schuck P and Demeler B. Direct sedimentation analysis of interference-optical data in analytical ultracentrifugation. Biophysical Journal 76:2288-2296 , 1999. [introduces algebraic noise decomposition allowing systematic noise and jitter to be directly modeled]
• Schuck P. Sedimentation analysis of non-interacting and self-associating solutes using numerical solutions to the Lamm equation. Biophysical Journal 75:1503-1512, 1998. [introduction of new moving grid finite element method, extension to self-associating systems by using predictor-corrector scheme]
• Schuck P, McPhee CE and Howlett GJ. Determination of sedimentation coefficients for small peptides. Biophysical Journal 74:466-474, 1998. [use of finite difference and Claverie's finite element method in Crank-Nicholson scheme for fast direct boundary modeling]