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A Suite of
Sedimentation Equilibrium/Velocity and Utilities Software |
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Authored by: Dr. Les Holladay
Available at:
Multifit (Sedimentation Equilibrium Software) -- Windows*
95/NT
- Mixedfit. This is for the simultaneous analysis of one to
12 Optima™ XL-A/XL-I analytical ultracentrifuge sedimentation
equilibrium absorbance or interference datafiles. The user can select
either a single ideal species, single non-ideal species, ideal
self-association, non-ideal self-association model, one of four ideal
isodesmic models, an ideal or non-ideal dimer-hexamer
isodesmic-hexamer model, or an ideal or nonideal monomer-dimer-hexamer
isodesmic-hexamer model. The baseline absorbances can be floated in
the curvefitting. The user needs to know the extinction coefficient of
the species at the wavelengths used and the fringe factor for
interference flies so that one may globally fit data at different
wavelengths, rotor speeds, optical systems, and loading
concentrations.
- Eqdata. This program will generate test data files for
Optima XL-A data analysis software. The type of system, data, noise,
etc. may all be specified. Graphs of Mw, Mz, etc. may be generated and
printed.
- Polyfit. This program implements Lechner's method for
estimating the molecular weight distribution of a polymer from
sedimentation equilibrium data from three to seven different initial
loading concentrations. See Lechner's manuscript in "Modern Analytical
Ultracentrifugation" for details.
- DelGElec. This program estimates the electrostatic
repulsion free energy in kJ/mol for two touching uniformly charges
spherical monomers using the Overbeek Verwey model. A short table is
sent to a memo pad, and the monomer molecular weight, the vbar, the
temperature, and the bounds for ionic strength and net charge may be
specified.
- Polydata. Computes synthetic datafiles for testing Polyfit.
EQFIT (Sedimentation Velocity and Utility Software) - Windows
3.x
- DENFIT. Reads in an AVIV file of absorbance (or
ellipticity) versus temperature. Estimates Td, DH
at Td, (and optionally DCp) from
the data using a nonlinear regression fit with the Simplex algorithm.
The user may allow either the pretransition value to be sloping, the
post-transition value, or both.
- DSCFIT. Reads in a DSC file (a sample is included)
Estimates Td, DH at Td, (and
optionally DCp) from the data
using a nonlinear regression fit with the Simplex algorithm. The user
has many choices of models.
- GdmFit. This program works much like DenFit, except that it
is for fitting guandinium chloride unfolding data. The data is
essentially any observable vs. molar guandinium chloride
concentration. The user has a choice of three extrapolation models.
For any model the baselines are floated in the curve fit if desired.
Sample datasets are *.gdm files.
- UreaFit. This program works much like GdmFit, except that
it is for fitting urea unfolding data. The data is essentially any
observable vs. molar urea concentration. The user has a choice of
three extrapolation models. For any model the baselines are floated in
the curve fit if desired. Sample datasets are *.ure files.
- NazMz. this program takes an interference sedimentation
equilibrium datafile and applies Nazarian's method to estimate the
apparent Z-average molecular weight across the solution column. This
is useful for heterogeneous systems, but not for single species
systems based on trial data.
(Sedimentation Velocity and Utility Software) - MS-DOS*
- A0CALC. Using an estimate for the buoyant molecular weight
as found by MIXEDFIT, this program computes the unredistributed
absorbance at 0 rpm. Useful for stability studies to track loss of
protein with time.
- ABSFILES and INTFILES. Lists either Optima XL-A absorbance
files with header info in a specified directory or Optima XL-I fringe
files in a specified directory.
- PLNSEDEQ. An interactive screen to help plan sedimentation
equilibrium runs. The program asks for the rotor speed, temperature,
partial specific volume, molecular weight, and asymmetry and estimates
the concentration gradient and the time required to reach equilibrium.
- SPEEDEQ. This program is an aid to reducing time to
sedimentation equilibrium by overspeeding. One enters molecular
parameters and the two times and speeds. The program estimates the
lack of departure from the true equilibrium pattern.
- PLOTAPEQ. Given molecular and cell parameters this program
plots out curves for approach-to-sedimentation equilibrium and the
final equilibrium distribution. A useful simulation tool for planning
experiments.
- AXIAL. A program to take hydrodynamic data and plot a
cross-section of the equivalent prolate ellipsoid. Useful simulation
and analysis tool.
- XLADATA. A program to manipulate Optima XL-A datafiles
outside the user interface.
- PLOTVEL. A program to plot sedimentation velocity profiles
given s, D, rotor speed, and the radial distance to the meniscus. A
useful simulation and planning program.
* All trademarks are the property of their respective owners. Where applicable,
the PCR process is covered by patents owned by Roche Molecular Systems, Inc.,
and F. Hoffmann-LaRoche, Ltd.
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