User contributions
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- 15:09, 11 August 2011 (diff | hist) . . (+323) . . N List of Graphs (Created page with "Sednterp will draw the following graphs: 1. Plots of asymmetry ratio as a function of hydration. 2. Diagrams of molecular shape where both a side axis and top axis view is show...")
- 15:08, 11 August 2011 (diff | hist) . . (+1,661) . . N Saving Data in Databases Form (Created page with "In this form, example, sample, buffer, or results information is saved as separate records in tables in a database file. This form not only saves information, but also serves as...")
- 15:08, 11 August 2011 (diff | hist) . . (+1,128) . . N Results (Created page with "The results form lists results of Sednterp calculations. To understand the results, read the theory section of this help file (and the references listed there for more in de...")
- 15:07, 11 August 2011 (diff | hist) . . (+1,510) . . N Limitations on Estimation of Hydration and Asymmetry (Created page with "One cannot determine accurate, unambiguous values for both the degree of hydration (δ1) and the ellipsoid axial ratios (a/b) from sedimentation experiments alone (Ref. 27 [[...")
- 15:05, 11 August 2011 (diff | hist) . . (0) . . N File:Equation24.GIF
- 15:02, 11 August 2011 (diff | hist) . . (+97) . . N Hydration (Created page with "Hydration is the ratio of the weight of bound water to the weight of the sample (grams per gram).")
- 15:01, 11 August 2011 (diff | hist) . . (+285) . . N Viscosity (Created page with "Viscosity is the measurement of resistance to bulk fluid flow. High viscosity indicates a thick substance like motor oil. Low viscosity indicates a very fluid substance. Viscosit...")
- 14:59, 11 August 2011 (diff | hist) . . (+95) . . N Density of Buffer (Created page with "Density is the measure of grams per milliliter of a substance. It is a basic physical property.")
- 14:59, 11 August 2011 (diff | hist) . . (+549) . . N Partial specific volume (Created page with "The partial specific volume has units of milliliters per gram (ml/g). In this sense it is simply the inverse of the density. however, partial specific volume is more strictly def...")
- 14:56, 11 August 2011 (diff | hist) . . (+3,542) . . N Calculating Molecular Weight (Created page with "Sednterp can use various methods to calculate molecular weight. First, the program may not calculate the molecular weight at all, but simply use the weight entered by the user....")
- 14:52, 11 August 2011 (diff | hist) . . (+3,860) . . N Converting s to s-20-w (Created page with "The sedimentation coefficient provides a rigorous hydrodynamic descriptor of a molecule. However, to be most useful in this regard, and prior to further interpretation, s* must ...")
- 14:50, 11 August 2011 (diff | hist) . . (0) . . N File:Equation3.GIF
- 14:50, 11 August 2011 (diff | hist) . . (+1,905) . . N Equations for s (Created page with "The apparent sedimentation coefficient is determined directly from the data: Rearrangement of equation 2 reveals that the sedimentation coefficient can be determined from the...")
- 14:48, 11 August 2011 (diff | hist) . . (+3,964) . . N Buffer Components Form (Created page with "The purpose of the Buffer Components form is to allow the user to enter components of a buffer and then to have Sednterp interpolate a buffer density and/or viscosity for the buf...")
- 14:47, 11 August 2011 (diff | hist) . . (+3,197) . . N Corrected (Created page with "The partial specific volume vbar is a measure of the change in the volume (in ml) of the solution per gram of solute. For typical proteins, any errors in vbar are magnified 3-fol...")
- 14:42, 11 August 2011 (diff | hist) . . (+1,361) . . N The Sample Section (Created page with "The sample section of the main form displays information particular to a sample (usually a biological macromolecule) that is the subject of experiment in the ultracentrifuge. Th...")
- 14:41, 11 August 2011 (diff | hist) . . (+18) . . List of Parameters for Input
- 14:41, 11 August 2011 (diff | hist) . . (+50) . . List of Parameters for Input
- 14:37, 11 August 2011 (diff | hist) . . (+12) . . Sedimentation coefficient corrected
- 14:37, 11 August 2011 (diff | hist) . . (+48) . . Sedimentation coefficient corrected
- 14:36, 11 August 2011 (diff | hist) . . (0) . . N File:Equation19.GIF
- 14:36, 11 August 2011 (diff | hist) . . (0) . . N File:Equation20.GIF
- 14:33, 11 August 2011 (diff | hist) . . (+20) . . Sedimentation coefficient corrected
- 14:32, 11 August 2011 (diff | hist) . . (+3,780) . . N Sedimentation coefficient corrected (Created page with "The sedimentation coefficient provides a rigorous hydrodynamic descriptor of a molecule. However, to be most useful in this regard, and prior to further interpretation, s* must ...")
- 14:26, 11 August 2011 (diff | hist) . . (+3,542) . . N Calculating the Molecular Weight (Created page with "Sednterp can use various methods to calculate molecular weight. First, the program may not calculate the molecular weight at all, but simply use the weight entered by the user....")
- 14:25, 11 August 2011 (diff | hist) . . (+628) . . N Buoyant molecular weight (Created page with "Sednterp will calculate the buoyant molecular weight of the sample according to the method chosen for calculating the molecular weight. The buoyant molecular weight is defined in...")
- 14:24, 11 August 2011 (diff | hist) . . (0) . . N File:Equation6-b.GIF
- 14:24, 11 August 2011 (diff | hist) . . (0) . . N File:Equation6.GIF
- 14:20, 11 August 2011 (diff | hist) . . (-1) . . Computed minimum radius
- 14:19, 11 August 2011 (diff | hist) . . (+134) . . N 34 (Created page with "H. Hoiland, 'Thermodynamic Data for Biochemistry and Biotechnology', H.-J. Hinz, ed., Springer-Verlag, Berlin, 1986, Chapter 2, p. 17.")
- 14:18, 11 August 2011 (diff | hist) . . (+146) . . N 32 (Created page with "S.E. Harding, 'Dynamic Properties of Biomolecular Assemblies', S.E. Harding and A.J. Rowe, eds., Royal Society of London, 1989, Chapter 2, p. xxx.")
- 14:17, 11 August 2011 (diff | hist) . . (+65) . . N 31 (Created page with "H.A. Scheraga an L. Mandelkern, J. Am. Chem. Soc., 1953, 75, 179.")
- 14:17, 11 August 2011 (diff | hist) . . (+163) . . N 30 (Created page with "D.C. Teller, E. Swanson and C. De Haen, 'Methods in Enzymology Volume 61', C.H.W. Hirs and S.N. Timasheff, eds., Academic Press, New York, 1979, Chapter 8, p. 103.")
- 14:15, 11 August 2011 (diff | hist) . . (+48) . . N 29 (Created page with "J.L. Oncley, Ann. N.Y. Acad. Sci. 1941, 41, 121.")
- 14:15, 11 August 2011 (diff | hist) . . (+140) . . N 27 (Created page with "Teller, D.C. 'Methods in Enzymology Volume XXVII', C.H.W. Hirs and S.N. Timasheff, eds., Academic Press, New York, 1973, Chapter 14, p. 346.")
- 14:13, 11 August 2011 (diff | hist) . . (+4,203) . . N Computed minimum radius (Created page with "This section deals with calculating the equivalent radius and all directly resulting values including the minimal frictional coefficient , the maximum diffusion coefficient, and ...")
- 14:10, 11 August 2011 (diff | hist) . . (0) . . N File:Equation21.GIF
- 14:10, 11 August 2011 (diff | hist) . . (0) . . N File:Equation22.GIF
- 14:10, 11 August 2011 (diff | hist) . . (0) . . N File:Equation23.GIF
- 14:04, 11 August 2011 (diff | hist) . . (+164) . . N 60 (Created page with "W.F. Stafford, Analytical Ultracentrifugation in Biochemistry and Polymer Science, Royal Society of Chemistry (Edited by S. Harding and A. Rowe), 1992, pp. 359-393.")
- 14:02, 11 August 2011 (diff | hist) . . (+24) . . Sedimentation coefficient
- 14:02, 11 August 2011 (diff | hist) . . (0) . . File:Equation26.GIF (uploaded a new version of "File:Equation26.GIF")
- 19:19, 9 August 2011 (diff | hist) . . (+57) . . N 42 (Created page with "J.C. Lee and S.N. Timasheff, Biochemistry, 1974, 13, 257.")
- 19:18, 9 August 2011 (diff | hist) . . (+61) . . N 54 (Created page with "I.D. Kuntz and W. Kauzman, Adv. Protein Chem., 1974, 28, 239.")
- 19:18, 9 August 2011 (diff | hist) . . (+44) . . N 51 (Created page with "I.D. Kuntz J. Am. Chem. Soc., 1971, 93, 514.")
- 19:15, 9 August 2011 (diff | hist) . . (-4) . . Estimating Hydration
- 19:14, 9 August 2011 (diff | hist) . . (+142) . . N 53 (Created page with "G.M. Mrevlishvili, 'Thermodynamic Data for Biochemistry and Biotechnology', H.-J. Hinz, ed., Springer-Verlag, Berlin, 1986, Chapter 5, p. 148.")
- 19:13, 9 August 2011 (diff | hist) . . (+155) . . N 55 (Created page with "H. Pessen and T.F. Kumosinski, 'Methods in Enzymology Volume 117', C.H.W. Hirs and S.N Timasheff, eds., Academic Press, New York, 1985, Chapter 14, p. 219.")
- 19:11, 9 August 2011 (diff | hist) . . (+46) . . Estimating Hydration
- 17:56, 9 August 2011 (diff | hist) . . (+1,972) . . N Estimating Hydration (Created page with "It has become common practice to specify a value of 0.25 or 0.3 for , with little justification. For unconjugated proteins, typical values of "hydrodynamic hydration" range betwe...")
- 17:56, 9 August 2011 (diff | hist) . . (0) . . N File:Equation26.GIF
- 17:43, 9 August 2011 (diff | hist) . . (+116) . . N 8 (Created page with "T. Svedberg 'The Ultracentrifuge', T. Svedberg and K.O. Pederson, eds., Johnson Reprint Corporation, New York, 1940.")
- 17:42, 9 August 2011 (diff | hist) . . (+162) . . N 48 (Created page with "J.F. Johnson, J.R. Martin and R.S. Porter, 'Physical methods of Chemistry', A. Weissberger and B.W. Rossiter, eds., Vol. 1, Part VI, Wiley, New York, 1977, p. 63.")
- 17:40, 9 August 2011 (diff | hist) . . (+160) . . N 47 (Created page with "J.T. Yang, 'Recent Advances in Protein Chemistry Volume 16', C.B. Anfinsen, M.L. Anson, K. Bailey, and J.T. Edsall, eds., Academic Press, New York, 1961, p.323.")
- 17:39, 9 August 2011 (diff | hist) . . (+89) . . Nm 17 (Created page with "H. Fujita, 'Foundations of Ultracentrigugal Analysis', J. Wiley and Sons, New York, 1975.")
- 17:38, 9 August 2011 (diff | hist) . . (+24) . . Calulating Viscosity
- 17:37, 9 August 2011 (diff | hist) . . (-54) . . Calulating Viscosity
- 17:37, 9 August 2011 (diff | hist) . . (+2,114) . . N Calulating Viscosity (Created page with "Viscosity is a measure of the energy dissipated in a fluid in order to maintain flow. In sedimentation, the flow of interest is the movement of the protein through the solvent. F...")
- 17:35, 9 August 2011 (diff | hist) . . (0) . . N File:Equation16.GIF
- 17:35, 9 August 2011 (diff | hist) . . (0) . . N File:Equation17.GIF
- 17:35, 9 August 2011 (diff | hist) . . (0) . . N File:Equation18.GIF
- 17:25, 9 August 2011 (diff | hist) . . (+62) . . N 45 (Created page with "F. Steckel and S. Szapiro, Trans. Faraday Soc., 1963, 59, 331.")
- 17:24, 9 August 2011 (diff | hist) . . (+127) . . N 44 (Created page with "R.C. Weast (editor), 'CRC Handbook of Chemistry and Physics, 67th Edition', CRC Press, Inc., Boca Raton, Florida, 1968, p. F-5.")
- 17:23, 9 August 2011 (diff | hist) . . (+165) . . N 46 (Created page with "M.L. Johnson and S.G. Frazsier, 'Methods in Enzymology Volume 117', C.H.W. Hirs and S.N. Timasheff, eds., Academic Press, Orlando, Florida, 1985, Chapter 16, p. 301.")
- 17:21, 9 August 2011 (diff | hist) . . (+41) . . Calculating Density
- 17:19, 9 August 2011 (diff | hist) . . (+4,416) . . N Calculating Density (Created page with "The first step Sednterp uses to calculate the density of a buffer is to calculate the density of the buffer at 20 degrees C. Then, the density is corrected for temperature assum...")
- 17:16, 9 August 2011 (diff | hist) . . (+3,964) . . N Buffer (Created page with "The purpose of the Buffer Components form is to allow the user to enter components of a buffer and then to have Sednterp interpolate a buffer density and/or viscosity for the buf...")
- 17:15, 9 August 2011 (diff | hist) . . (+4,791) . . N Sample (Created page with "The sample composition form allows the user to enter the composition of a protein and also allows access to computed values from the composition. The amino acid composition is li...")
- 17:13, 9 August 2011 (diff | hist) . . (+175) . . N 35 (Created page with "J.H.C. Steele, C. Tanford and J.A. Reynolds, 'Methods in Enzymology Volume 48', C.H.W. Hirs and S.N. Timasheff, eds., Academic Press, Orlando, Florida, 1978, Chapter 2, p. 18.")
- 17:12, 9 August 2011 (diff | hist) . . (+205) . . Nm 59 (Created page with "T.M. Laue, B.D. Shah, T.M. Ridgeway and S.L. Pelletier, Analyticall Ultracentrifugation in Biochemistry and Polymer Science, Royal Society of Chemistry (Edited by S. Harding and ...")
- 17:10, 9 August 2011 (diff | hist) . . (+73) . . Calculating vbar Estimates
- 17:08, 9 August 2011 (diff | hist) . . (+3,092) . . N Calculating vbar Estimates (Created page with "he partial specific volume is a measure of the change in the volume (in ml) of the solution per gram of solute. For typical proteins, any errors in are magnified 3-fold in the ...")
- 17:06, 9 August 2011 (diff | hist) . . (+1) . . List of Interpolations Available
- 17:06, 9 August 2011 (diff | hist) . . (+677) . . N List of Interpolations Available (Created page with "Sednterp will interpolate values for the following properties. {| !Property !Input !Theory !Form |- |Vbar |Amino Acids and conjugates, temp. |Calculating vbar Estimates |[[S...")
- 14:57, 9 August 2011 (diff | hist) . . (+422) . . N Interpolation (Created page with "In the program Sednterp, interpolation refers to the estimation of physical parameters from standard tables and user entered information. In most cases, Sednterp uses a power se...")
- 14:57, 9 August 2011 (diff | hist) . . (+1,126) . . List of Results
- 14:49, 9 August 2011 (diff | hist) . . (+553) . . N List of Results (Created page with "Results are molecular parameters computed by Sednterp from the equations described in the theory section. To understand the results, the theory section ought to be read at lengt...")
- 14:47, 9 August 2011 (diff | hist) . . (+589) . . N Sigma (Created page with "In equilibrium sedimentation experiments, the reduced apparent molecular weight. This is the term which is directly measured by experiment; often it is fit by nonlinear least sq...")
- 14:47, 9 August 2011 (diff | hist) . . (+212) . . N Interpretation (Created page with "In the program Sednterp, interpretation refers to the computation of molecular structural properties from (σ) sigma, s and the experimental conditions. See also: [[Li...")
- 14:45, 9 August 2011 (diff | hist) . . (-1) . . m Theory of Computer Aided Interpretation of Sedimentation Data
- 14:45, 9 August 2011 (diff | hist) . . (+2,046) . . N Theory of Computer Aided Interpretation of Sedimentation Data (Created page with "The theory described here focuses on the interpretation of sedimentation data for purified proteins, glycoproteins or lipoproteins exhibiting relatively simple behavior in aq...")
- 14:00, 9 August 2011 (diff | hist) . . (+1,750) . . N Interpolate a viscosity (Created page with "To interpolate a density or viscosity press the compute button on either the buffer density or buffer viscosity frames. The buffer components form will appear. The same form wi...")
- 14:00, 9 August 2011 (diff | hist) . . (+968) . . N Calculating Estimates of Hydration and Asymmetry (Created page with "Comparing the minimal frictional coefficient with results from a Sedimentation Velocity experiment will yield estimates of maximum hydration and maximum asymmetry. Please not...")
- 13:59, 9 August 2011 (diff | hist) . . (+45) . . N 33 (Created page with "D.C. Teller, Nature (London), 1976, 260, 729.")
- 13:58, 9 August 2011 (diff | hist) . . (+156) . . N 28 (Created page with "T.F. Kumosinski and H. Pessen, 'Methods in Enzymology Volume 117', C.H.W. Hirs and S.N. Timasheff, eds., Academic Press, New York, 1985, Chapter 11, p. 154.")
- 13:57, 9 August 2011 (diff | hist) . . (+1,710) . . N Minimal frictional coefficient (Created page with "The equivalent radius is the radius of an anhydrous sphere of equivalent volume to a given protein. Given Mr and vbar, a vbar-dependent equivalent radius can be computed. An emp...")
- 13:54, 9 August 2011 (diff | hist) . . (+972) . . N Calculating the Equivalent Radius (Created page with "Comparing the minimal frictional coefficient with results from a Sedimentation Velocity experiment will yield estimates of maximum hydration and maximum asymmetry. Please no...")
- 13:52, 9 August 2011 (diff | hist) . . (+307) . . N Enter a molecular weight (Created page with "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 button (alt-m shortcut keystr...")
- 13:52, 9 August 2011 (diff | hist) . . (+1,750) . . N An interpolated ρ (Created page with "To interpolate a density or viscosity press the compute button on either the buffer density or buffer viscosity frames. The buffer components form will appear. The same form wi...")
- 13:52, 9 August 2011 (diff | hist) . . (0) . . Data from a sedimentation equilibrium experiment
- 13:51, 9 August 2011 (diff | hist) . . (+1,254) . . N An interpolated (Created page with "Sednterp will interpolate the partial specific volume of proteins from the composition of the protein and its ligands. Optionally, Sednterp will also compute the molecular weigh...")
- 13:42, 9 August 2011 (diff | hist) . . (+91) . . N 26 (Created page with "M.L. Johnson, J.C. Correia, D.A. Yphantis and H.R. Halvorson Biophysical J., 1981, 36, 575.")
- 13:41, 9 August 2011 (diff | hist) . . (+84) . . N 2 (Created page with "J.W. Williams, K.E. Van Holde, R.L. Baldwin, and H. Fujita, Chem. Rev., 1958,58,715.")
- 13:40, 9 August 2011 (diff | hist) . . (+1,869) . . Table of symbols
- 21:01, 8 August 2011 (diff | hist) . . (+349) . . Table of symbols
- 20:57, 8 August 2011 (diff | hist) . . (+3) . . Table of symbols
- 20:56, 8 August 2011 (diff | hist) . . (+30) . . Table of symbols
- 20:56, 8 August 2011 (diff | hist) . . (-1) . . Table of symbols
- 20:55, 8 August 2011 (diff | hist) . . (+75) . . N Table of symbols (Created page with "{| |+!List of Symbols Used|- ! align="left"|Symbol ! Description ! Units |}")
- 20:49, 8 August 2011 (diff | hist) . . (+59) . . N 25 (Created page with "D.A Yphantis and D.F. Waugh, J. Phys. Chem., 1956, 60, 623.")
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