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SVEDBERG

What is SVEDBERG?

SVEDBERG is a Windows program for whole-boundary analysis of sedimentation velocity data. It fits directly to the raw scans (usually spanning the entire run) to derive the sedimentation coefficient and molar mass (or, if you prefer, sedimentation coefficient and diffusion coefficient) for up to 6 independent species (mixtures of up to 6 components).

The program is designed to be easy to use, even for novices, yet it also offers many options for the 'power user' when they are needed. It uses multi-page analysis 'documents' and a familiar user interface with toolbars and buttons, making it similar to other Windows programs to reduce the learning curve. It also incorporates a number of intelligent 'wizards' that automatically accomplish tasks such as locating the meniscus position, removal of systematic noise ("jitter") and fringe jumps from interference scans, and even making reasonable initial guesses for the molecular parameters.

This is not a package that tries to do everything---its purpose is to implement one particular approach (analysis of single species and mixtures), do that very well and very easily, and do it in a highly reproducible and well-documented manner. It is not intended to be able to handle samples where the data is strongly influenced by dynamic reversible-association reactions (interacting boundaries). However when reversible interactions are strong enough that a reversible oligomer or complex can be treated as a single species then SVEDBERG is quite useful for identifying the molar mass (stoichiometry) of that species, which in turn can be a very useful input to analysis of data using other software acquired under conditions where the dynamic interactions are more significant.

The success of this approach is demonstrated by its use in 140+ known publications. More significantly, many of these are from intermittent or casual users of AUC, proving you don't have to devote years to learning data analysis to successfully answer important research questions with SV.

The program is now distributed as "freeware" and requires no registration. The only restriction is that it cannot be sold or packaged with other commercial software. The author asks only that you cite it properly when publishing your analyzed results.

Major features:

Modern multi-document, Explorer-style user interface

	toolbar with standard buttons for file open, file save, etc.
	multiple analyses can be open simultaneously,
	Explorer-like navigation tree to move to specific analysis pages (analysis steps) and between analysis documents
	click-and-drag setting of meniscus marker, data limits, cell base position, etc. [see image below]

Allows direct conversion of a c(s) distribution from SEDFIT into an equivalent mixture model, allowing determination of true confidence intervals for all the species fractions and sedimentation coefficients simultaneously

	when desired you can modify the constant f/f₀ ratio constraints (for example using oligomer constraints instead) or try removing the constraint altogether to see whether the mass of a minor component can be determined independently
	SVEDBERG can load the data range and other parameters used in the c(s) fit

Allows use of any of the current methods for handling systematic noise in the raw scans:

	either fitting the TIN (time-invariant noise), scan differencing, or a simple baseline offset
	for interference or pseudo-absorbance scans, either arithmetic removal of "jitter" (radially-invariant noise, RIN) at a fixed region of the cell or fitting of the RIN

Improved Lamm equation solution gives s, D, and M values for each species with theoretical accuracy of better than 0.1%, and will work for small peptides

Evaluates fitted parameter confidence intervals using any of three orthogonal approaches: F statistics, the bootstrap method, or the Monte Carlo method

For multi-species fits you can choose whether to fit the total concentration and species fractions, or to fit the loading concentration for each species

Species 1 can optionally have a negative concentration to handle signals from un-matched buffer components

Generates a log file that records every step of the data analysis, every option selected, every intermediate fitting result (including a table and graph), when it was done, and by whom (for computers with authenticated log-in servers)

Generates nicely formatted printed reports with tables, and which document every factor that influences the results. These reports (with graphs) can be pasted into your word processor or an electronic lab notebook

Creates 9 types of publication-quality graphs of fit results, including 2-D gray scale or color 'bitmap' residual plots that are re-scalable (not fixed bitmaps) and with a color scale key

2-D contour 'bitmap' residual plot

True local Help file to give context-sensitive Help for each dialog box or control, with extensive tutorials and a searchable index. (A PDF file to print a user manual is also available to registered users)

Saved analysis documents record every parameter, including the raw data, in a single file so you can re-load your analysis back to exactly the same state

Analysis documents appear in your 'My Recent Documents' folder, just like your other documents

Download it now! | User List | Publication List | Revision history | back to top

How does SVEDBERG differ from the multi-component models in Peter Schuck's SEDFIT?

SEDFIT is an excellent program with many strengths. It's 'non-interacting discrete species' model is essentially equivalent to the model used in SVEDBERG, except it derives the theoretical fits via finite-element numerical methods rather than approximate analytical functions. Both approaches can give an accuracy of better than 1% for hydrodynamic properties, i.e. more than sufficient for any real experiment.

The analytical function approach used in SVEDBERG is faster to compute and its Gauss-Newton fitting algorithm often converges more rapidly (especially when many components are present) than the algorithms available in SEDFIT. Thus overall SVEDBERG is generally faster and easier to use, and can successfully converge on multi-species fits in situations where SEDFIT fails to converge on a solution.

Perhaps more significantly, SVEDBERG always gives error estimates for all the fitted parameters, and can derive robust confidence limits for all parameters when desired. SEDFIT never gives error estimates or true confidence limits for concentration or species fractions, and can only derive confidence limits for s or M for a single component and through a lengthy procedure.

Another key difference is that SVEDBERG provides comprehensive, well-formatted printed reports that completely document the analysis, and which can be pasted into a word processor or electronic lab notebook. SEDFIT has no reporting capability.

SVEDBERG saves all data and parameters into a single file that can be quickly restored. SEDFIT has an incomplete ability to restore all aspects of previous analyses, making it difficult to reproduce what you have done.

Some other advantages of SVEDBERG over SEDFIT:

	for multi-species fits the relative masses or sedimentation coefficients can be constrained to values appropriate for a series of oligomers
	true context-sensitive, indexed and searchable HELP file
	accurate, easy, and reproducible setting of meniscus position and data fitting limits
	superior graphs that can be printed, exported or saved to disk, with full graph scaling and customization capabilities
	handles conversions of raw s and D values to s_20,w and D_20,w
	superior ease-of-use

Some advantages of SEDFIT over SVEDBERG:

	includes models for self-association and non-ideal sedimentation
	does floatation analysis as well as sedimentation
	handles compressible solvents and gradient-forming co-solutes
	can correct for boundary spreading during rotor acceleration

System Requirements

SVEDBERG 7 runs under Windows XP, Vista, 7, 8, or 10. Use via Windows dual-boot configurations on MacIntosh systems usually works fine, but is not officially supported or guaranteed.

This program also requires the Microsoft .NET framework to be present on the computer. This is usually already true for newer computers. If it is not already present, this is detected during installation and a link is given so it can be downloaded from Microsoft and installed.

Although SVEDBERG will run correctly at a 640x480 (VGA) video resolution, a resolution of 1024 x 768 or higher is highly recommended.

Program installation requires approximately 11 MBytes of disk space (most of which is for the comprehensive Help file).

How should I cite this program?

The primary citation for this program is:

Philo, J. S. (1997). An improved function for fitting sedimentation velocity data for low-molecular-weight solutes. Biophys. J. 72, 435-444.

The program itself should simply be cited as SVEDBERG (by convention program names are normally all capitals) by John Philo, with the version number.

The citation for the Behlke fitting function used by default starting with version 7.0.0 is:

Behlke, J. and Ristau, O. (2002). A new approximate whole boundary solution of the Lamm differential equation for the analysis of sedimentation velocity experiments. Biophys. Chem. 95, 59-68.

The citation for the multi-section option for scan differencing (delta-c mode) is:

Philo, J. S. (2011). Limiting the sedimentation coefficient for sedimentation velocity data analysis: Partial boundary modeling and g(s*) approaches revisited. Anal. Biochem. 412, 189-202.