[[Category:Sednterp]] [[Category:Table of Contents]]
...dfdownload.png|link=http://bitcwiki.sr.unh.edu/index.php?title=Category:Sednterp&action=pdfbook]]
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[[Category:Sednterp]]'''I. Introduction.'''
1. [[General Information on Sednterp]].
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[[Category:Sednterp]][[Category:Introduction]]
In this section of the help file, basic instructions for the use of Sednterp are given. It is assumed that the user reading these instructions is somew
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[[Category:Sednterp]][[Category:Introduction]]
The purpose of Sednterp is to automatically preform calculations on data connected to ultracentrifu
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[[Category:Sednterp]][[Category:Introduction]]
Sednterp can compute the molecular weight from:
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[[Category:Sednterp]]
...mpute the weight of a protein from its composition. To use this method in Sednterp, press the From Composition button (alt-c shortcut keystroke). The Sample
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[[Category:Sednterp]]
...dard tables of single component buffer data have been fit by polynomials. Sednterp computes density increments for each component at the user entered concentr
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[[Category:Sednterp]]The first step Sednterp uses to calculate the density of a buffer is to calculate the density of th
...rom the most parsimonious polynomial providing an adequate fit are used by Sednterp. Adequacy of the fits were judged by the following criteria: 1) the r.m.s.
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[[Category:Sednterp]]The sample composition form allows the user to enter the composition of a
...atibility with pre-release versions of Sednterp. With current versions of Sednterp it is not necessary to save composition data in such files, since the compo
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[[Category:Sednterp]][[Category:Sednterp Program Control and Screens]]
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[[Category:Sednterp]]
...tal information, but instead contains essential extrapolation data for the Sednterp program. Users can create their own experimental information databases in
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[[Category:Sednterp]]In this form, example, sample, buffer, or results information is saved as
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[[Category:Sednterp]]
...tal information, but instead contains essential extrapolation data for the Sednterp program. Users can create their own experimental information databases in
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[[Category:Sednterp]]
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[[Category:Sednterp]]The partial specific volume is a measure of the change in the volume (in
...and the carboxy-terminal hydroxyl (and that is the implementation used in Sednterp).
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[[Category:Sednterp]][[Category:Introduction]]
...proteins from the composition of the protein and its ligands. Optionally, Sednterp will also compute the molecular weight from this also.
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[[Category:Sednterp]][[Category:Introduction]]
...density and viscosity data has not yet been fit to the polynomial function Sednterp uses to interpolate these values. With experimental measurements, new comp
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[[Category:Sednterp]][[Category:Introduction]]
...an average estimating formula worked out by Teller (Ref. [[28]] [[33]]). Sednterp automatically calculates the equivalent radius when [[Mr is computed]]. It
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[[Category:Sednterp]]Sednterp can compute the molecular weight from:
Sednterp will let you [[enter a molecular weight]] yourself to use in latter computa
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[[Category:Sednterp]]
Given a certain temperature, rotor speed, and σ, Sednterp will use default approximate values of vbar and ρ automatically to compute
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[[Category:Sednterp]]The reduced apparent molecular weight, σ, is directly available from sedi
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[[Category:Sednterp]]
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[[Category:Sednterp]]
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[[Category:Sednterp]][[Category:Introduction]]
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[[Category:Sednterp]]
...proteins from the composition of the protein and its ligands. Optionally, Sednterp will also compute the molecular weight from this also.
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[[Category:Sednterp]]
...density and viscosity data has not yet been fit to the polynomial function Sednterp uses to interpolate these values. With experimental measurements, new comp
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[[Category:Sednterp]]
For those cases when the molecular weight of a sample is known, Sednterp allows the user to enter a molecular weight directly. Click on the Exact M
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
...if some information is available about either hydration or asymmetry then Sednterp will use this to calculate better estimates of the other value. For instanc
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[[Category:Sednterp]]
...an average estimating formula worked out by Teller (Ref. [[28]] [[33]]). Sednterp automatically calculates the equivalent radius when [[Mr is computed]]. It
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[[Category:Sednterp]]
...if some information is available about either hydration or asymmetry then Sednterp will use this to calculate better estimates of the other value. For instanc
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[[Category:Sednterp]]To interpolate a density or viscosity press the compute button on either t
...density and viscosity data has not yet been fit to the polynomial function Sednterp uses to interpolate these values. With experimental measurements, new comp
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[[Category:Sednterp]]
...ll as the protein's partial specific volume. Such data may be entered into Sednterp directly (and temperature corrections computed) or the program may use vari
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[[Category:Sednterp]][[Category:Introduction]]
In the program Sednterp, interpretation refers to the computation of molecular structural propertie
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[[Category:Sednterp]]
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[[Category:Sednterp]][[Category:Introduction]]
Results are molecular parameters computed by Sednterp from the equations described in the theory section. To understand the resu
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[[Category:Sednterp]]
...uses a power series approximation of standard tabular data. For example, Sednterp will interpolate the density of a solution from the concentration of solute
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[[Category:Sednterp]][[Category:Introduction]]
Sednterp will interpolate values for the following properties.
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[[Category:Sednterp]]
...and the carboxy-terminal hydroxyl (and that is the implementation used in Sednterp).
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[[Category:Sednterp]][[Category:Introduction]]
...atibility with pre-release versions of Sednterp. With current versions of Sednterp it is not necessary to save composition data in such files, since the compo
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[[Category:Sednterp]]
...dard tables of single component buffer data have been fit by polynomials. Sednterp computes density increments for each component at the user entered concentr
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[[Category:Sednterp]]
The first step Sednterp uses to calculate the density of a buffer is to calculate the density of th
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[[Category:Sednterp]]
Sednterp can interpolate the viscosity of a buffer from viscosity table data in the
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
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[[Category:Sednterp]][[Category:Introduction]]
...ysical parameters of common buffers used in sedimentation experiments. The Sednterp program was developed at AMGEN by John Philo with the help of David Hayes a
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[[Category:Sednterp]][[Category:Introduction]]
The Sednterp program helps to interpret σ's found by other programs (such as NONLIN). T
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[[Category:Sednterp]][[Category:Introduction]]
The Sednterp program requires the weight of the solute and s for various shape estimates
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[[Category:Sednterp]][[Category:Introduction]]
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[[Category:Sednterp]][[Category:Introduction]]
...p uses a power series approximation of standard tabular data. For example, Sednterp will interpolate the density of a solution from the concentration of solute
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[[Category:Sednterp]][[Category:Introduction]]
...g users to compile reports and make use of the data in programs other than Sednterp.
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[[Category:Sednterp]][[Category:Introduction]]
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[[Category:Sednterp]][[Category:Introduction]]
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
...ll as the protein's partial specific volume. Such data may be entered into Sednterp directly (and temperature corrections computed) or the program may use vari
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[[Category:Sednterp]]
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[[Category:Sednterp]][[Category:Introduction]]
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[[Category:Sednterp]][[Category:Introduction]]
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[[Category:Sednterp]][[Category:Introduction]]
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[[Category:Sednterp]][[Category:Introduction]]
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[[Category:Sednterp]]
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[[Category:Sednterp]]
...omatic defaults, a quick answer is obtained by entering sigma and RPM. If Sednterp does not have enough information to compute the molecular weight, a stop si
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[[Category:Sednterp]]
...atibility with pre-release versions of Sednterp. With current versions of Sednterp it is not necessary to save composition data in such files, since the compo
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[[Category:Sednterp]][[Category:Sednterp Program Control and Screens]]
...tal information, but instead contains essential extrapolation data for the Sednterp program. Users can create their own experimental information databases in
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[[Category:Sednterp]]The apparent sedimentation coefficient is determined directly from the dat
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[[Category:Sednterp]]
...8]] [[29]] [[30]] [[31]] [[32]]) from the analytical ultracentrifuge. The Sednterp program assumes that only sedimentation data are available, and methods tha
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[[Category:Sednterp]]Sednterp will calculate the buoyant molecular weight of the sample according to the
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[[Category:Sednterp]]
Sednterp can use various methods to calculate molecular weight.
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[[Category:Sednterp]]
...l in comparing the sedimentation behavior of different proteins. Moreover Sednterp must use s20w in calculating the limits of hydration and estimating the asy
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[[Category:Sednterp]][[Category:Sednterp Program Control and Screens]]
The choice of vbar used by Sednterp in its calculations is indicated by the one green underlined button.
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[[Category:Sednterp]]
...and the carboxy-terminal hydroxyl (and that is the implementation used in Sednterp).
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[[Category:Sednterp]][[Category:Sednterp Program Control and Screens]]
...dard tables of single component buffer data have been fit by polynomials. Sednterp computes density increments for each component at the user entered concentr
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[[Category:Sednterp]]
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
...l in comparing the sedimentation behavior of different proteins. Moreover Sednterp must use s20w in calculating the limits of hydration and estimating the asy
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[[Category:Sednterp]]
Sednterp can use various methods to calculate molecular weight.
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[[Category:Sednterp]]
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[[Category:Sednterp]]
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[[Category:Sednterp]]
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[[Category:Sednterp]]
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
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[[Category:Sednterp]]
The results form lists results of Sednterp calculations. To understand the results, read the [[theory section]] of th
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[[Category:Sednterp]]
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[[Category:Sednterp]][[Category:Introduction]]
Sednterp will draw the following graphs:
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[[Category:Sednterp]][[Category:Sednterp Program Control and Screens]]
Various graphs are available from the results and composition forms in Sednterp. All of these graphs use a standard form with many options for formatting
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[[Category:Sednterp]]
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[[Category:Sednterp]]
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[[Category:Sednterp]]
The results form lists results of Sednterp calculations. To understand the results, read the [[theory section]] of th
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[[Category:Sednterp]][[Category:Introduction]]
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[[Category:Sednterp]][[Category:Introduction]]
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[[Category:Sednterp]]
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[[Category:Sednterp]][[Category:Introduction]]
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
...ground useful to understand Sednterp. In a few cases the formulae used in Sednterp differ from those in Ref. [[59]] (mostly due to correction of typographical
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
...in's hydration and asymmetry. While none of the calculations is difficult, Sednterp assembles all of them into one program to facilitate data interpretation. T
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[[Category:Sednterp]]
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
...histicated algorithms. Users who often use an algorithm not implemented in Sednterp should [[contact]] the programmers; portions of the source code are availab
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[[Category:Sednterp]]The first step Sednterp uses to calculate the density of a buffer is to calculate the density of th
...rom the most parsimonious polynomial providing an adequate fit are used by Sednterp. Adequacy of the fits were judged by the following criteria: 1) the r.m.s.
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[[Category:Sednterp]]For general questions regarding interpretation of sedimentation data and t
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
Sednterp can use various methods to calculate molecular weight.
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
Sednterp will calculate the buoyant molecular weight of the sample according to the
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
...and the carboxy-terminal hydroxyl (and that is the implementation used in Sednterp).
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
...by equation 9 (ref. [[37]]) replaces vbar in all calculations performed by Sednterp.
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
The first step Sednterp uses to calculate the density of a buffer is to calculate the density of th
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
The first step Sednterp uses to calculate the density of a buffer is to calculate the density of th
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[[Category:Sednterp]]The first step Sednterp uses to calculate the density of a buffer is to calculate the density of th
...rom the most parsimonious polynomial providing an adequate fit are used by Sednterp. Adequacy of the fits were judged by the following criteria: 1) the r.m.s.
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
Sednterp can interpolate the viscosity of a buffer from viscosity table data in the
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
Sednterp performs both variations of this calculation automatically in the Results f
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
...ion for both the prolate and oblate ellipsoid models will be calculated by Sednterp. To do this, the frictional coefficient ratios (prolate= and oblate=) corr
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[[Category:Sednterp]]This section deals with calculating the equivalent radius and all directly
...8]] [[29]] [[30]] [[31]] [[32]]) from the analytical ultracentrifuge. The Sednterp program assumes that only sedimentation data are available, and methods tha
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[[Category:Sednterp]][[Category:References]]
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[[Category:Sednterp]][[Category:Sednterp Program Control and Screens]]
...rs from experimental information. The purpose of most of the [[forms]] in Sednterp is to allow the user to enter or to see information.
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[[Category:Sednterp]]A form is a window that contains any number of Microsoft Windows or Visual
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[[Category:Sednterp]][[Category:Sednterp Program Control and Screens]]
...atibility with pre-release versions of Sednterp. With current versions of Sednterp it is not necessary to save composition data in such files, since the compo
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[[Category:Sednterp]][[Category:Sednterp Program Control and Screens]]
The results form lists results of Sednterp calculations. To understand the results, read the [[theory section]] of thi
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[[Category:Sednterp]][[Category:Sednterp Program Control and Screens]]
The choice of vbar used by Sednterp in its calculations is indicated by the one green underlined button.
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...ndard tables of single component buffer data have been fit by polynomials. Sednterp computes density increments for each component at the user entered concentr
...recreate the buffer components from one mode to the other. If this occurs, Sednterp will warn the user with a message box. If the user has data and a polynomia
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[[Category:Sednterp]][[Category:Sednterp Program Control and Screens]]
...omatic defaults, a quick answer is obtained by entering sigma and RPM. If Sednterp does not have enough information to compute the molecular weight, a stop si
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[[Category:Sednterp]][[Category:Sednterp Program Control and Screens]]
...b data base to modify or add to the calculation/interpolation data used by Sednterp.
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[[Category:Sednterp]][[Category:Sednterp Program Control and Screens]]
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[[Category:Sednterp]]
The results form lists results of Sednterp calculations. To understand the results, read the [[theory section]] of th
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[[Category:Sednterp]][[Category:Sednterp Program Control and Screens]]
The overall strategy of the Sednterp program is to allow the user to enter information quickly and easily.
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[[Category:Sednterp]][[Category:Sednterp Program Control and Screens]]
One strategy of Sednterp is to have one main form with a minimum number of elements. Optional info
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[[Category:Sednterp]][[Category:Sednterp Program Control and Screens]]
The Sednterp program allows the user to control the information and the order of computa
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[[Category:Sednterp]][[Category:Sednterp Program Control and Screens]]
...use of these defaults limit the accuracy of the calculations performed by Sednterp.
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
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[[Category:Sednterp]]
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
...ion of the tabulated data for a/b as a function of f/f0. (Ref. [[18]]) In Sednterp, the coefficients of the corresponding power series in [[File: Equationer.G
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[[Category:Sednterp]]
...8]] [[29]] [[30]] [[31]] [[32]]) from the analytical ultracentrifuge. The Sednterp program assumes that only sedimentation data are available, and methods tha
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[[Category:Sednterp]][[Category:Theory of Computer Aided Interpretation of Sedimentation Data]]
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[[Category:Sednterp]]
...density and viscosity data has not yet been fit to the polynomial function Sednterp uses to interpolate these values. With experimental measurements, new comp
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...b data base to modify or add to the calculation/interpolation data used by Sednterp.
...ted by the user. If this data base is modified, two different versions of Sednterp (or one version at a later date) will give divergent estimates for buffer d
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[[Category:Sednterp]][[Category:Introduction]]
...if some information is available about either hydration or asymmetry then Sednterp will use this to calculate better estimates of the other value. For instanc
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[[Category:Sednterp]]
Sednterp is available for the following platforms for the current 20130519 Beta vers
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[[Category:Sednterp]]
...ant you access to the Sednterp bug-reporting project. Please send email to sednterp@spork.sr.unh.edu after you have confirmed your account. Please indicate you
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[[Category:Sednterp]][[Category:Sednterp Web]]
...Web application is created using the same back end for calculations as the Sednterp v2.0 desktop application. The web page utilizes the same daemon, module fil
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[[Category:Sednterp]]
...atibility with pre-release versions of Sednterp. With current versions of Sednterp it is not necessary to save composition data in such files, since the compo
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[[Category:Sednterp]]
...atibility with pre-release versions of Sednterp. With current versions of Sednterp it is not necessary to save composition data in such files, since the compo
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[[Category:Sednterp]]
...tal information, but instead contains essential extrapolation data for the Sednterp program. Users can create their own experimental information databases in
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[[Category:Sednterp]]
...dard tables of single component buffer data have been fit by polynomials. Sednterp computes density increments for each component at the user entered concentr
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[[Category:Sednterp]][[Category:Introduction]]
Sednterp uses conventions for the three letter file ending for the various files imp
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To import your sednterp database from Sednterp version 1 into Sednterp version 2 you will need to do the following
...pop up. Click Set Source Folder and point it to you folder where you have Sednterp version 1 installed.
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...all done in a module file, which is essentially a javaScript file, on load Sednterp searches for the module file with greatest version number and uses it for c
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To update Sednterp to the newest release through Sednterp you will need to do the following.
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[[Category:Sednterp]][[Category:Sednterp Web]]
...nterp web, as well for security reasons. Instead then users can save their Sednterp web session to an xml file which they can then use load to for later use th
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[[Category:Sednterp]][[Category:Sednterp Web]]
On every tab of Sednterp web there are two buttons under the calculations right hand corner Called "
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[[Category:Sednterp]][[Category:Modules]]
...atform tools to help create the module in the form of developer tools. The Sednterp distribution comes with an example module which can be edited so users can
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[[Category:Sednterp]][[Category:Modules]]
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[[Category:Sednterp]][[Category:Modules]]
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[[Category:Sednterp modules]]
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