User contributions
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- 19:32, 15 August 2011 (diff | hist) . . (+1) . . Molecular Weight
- 19:31, 15 August 2011 (diff | hist) . . (+53) . . Molecular Weight
- 18:06, 15 August 2011 (diff | hist) . . (+969) . . N 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 no...")
- 19:08, 11 August 2011 (diff | hist) . . (+3,540) . . N Estimating Database (Created page with "This menu allows the user to access the phyconst.mdb data base to modify or add to the calculation/interpolation data used by Sednterp. The two things most likely to be modified...")
- 18:58, 11 August 2011 (diff | hist) . . (+1,750) . . N Interpolating a Density or 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...")
- 18:55, 11 August 2011 (diff | hist) . . (0) . . N File:Equation36.GIF
- 18:55, 11 August 2011 (diff | hist) . . (0) . . N File:Equation3l.GIF
- 18:55, 11 August 2011 (diff | hist) . . (0) . . N File:Molarequation.GIF
- 18:54, 11 August 2011 (diff | hist) . . (+1,080) . . N Calculating Cylindrical Asymmetry (Created page with "The proper hydrodynamic model for molecules that exhibit an elongated shape with a uniform thickness is the cylinder. The frictional coefficient for a cylinder is: Equation 36: ...")
- 18:49, 11 August 2011 (diff | hist) . . (+4,202) . . N Teller's empirical estimates (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 ...")
- 18:47, 11 August 2011 (diff | hist) . . (+74) . . Calculating Ellipsoid Asymmetry
- 18:47, 11 August 2011 (diff | hist) . . (0) . . N File:Equation31.GIF
- 18:46, 11 August 2011 (diff | hist) . . (0) . . N File:Equation32.GIF
- 18:46, 11 August 2011 (diff | hist) . . (0) . . N File:Equation35.GIF
- 18:46, 11 August 2011 (diff | hist) . . (0) . . N File:Equationer.GIF
- 18:46, 11 August 2011 (diff | hist) . . (+1,366) . . N Calculating Ellipsoid Asymmetry (Created page with "The maximum axial ratio of the prolate ellipsoid of revolution (a/b)p,max and the oblate ellipsoid of revolution (a/b)o,max can be determined using a power series approximation o...")
- 18:37, 11 August 2011 (diff | hist) . . (0) . . Stokes radius
- 18:37, 11 August 2011 (diff | hist) . . (+644) . . N Stokes radius (Created page with "The Stokes radius (also often called the hydrodynamic radius) is the radius of a spherical particle that has the same frictional coefficient, f, as that of the current sample (an...")
- 18:32, 11 August 2011 (diff | hist) . . (0) . . N File:Equationist.GIF
- 18:32, 11 August 2011 (diff | hist) . . (+350) . . N Calculating the Stokes Radius (Created page with "The Stokes radius can be calculated from several relationships, such as File: Equationist.GIF Note that this calculation does not depend on whether you choose the vbar ...")
- 18:28, 11 August 2011 (diff | hist) . . (+1) . . Sednterp Uses Default Values
- 18:28, 11 August 2011 (diff | hist) . . (+1,514) . . N Sednterp Uses Default Values (Created page with "Sednterp uses default values for many parameters that may be entered by the user. The use of these defaults limit the accuracy of the calculations performed by Sednterp. Defaul...")
- 18:27, 11 August 2011 (diff | hist) . . (+455) . . N The User Controls Program Information and Flow (Created page with "The Sednterp program allows the user to control the information and the order of computation used by the program. Choices for program flow are indicated by the green boxes under...")
- 18:27, 11 August 2011 (diff | hist) . . (+194) . . N A Sparse Main Form Leads to Other Program Elements (Created page with "One strategy of Sednterp is to have one main form with a minimum number of elements. Optional information is entered on separate forms. The following help topics describe the ...")
- 18:16, 11 August 2011 (diff | hist) . . (+2,308) . . N Programming Strategy (Created page with "The overall strategy of the Sednterp program is to allow the user to enter information quickly and easily. The program will default to guessed values for all parameters that ad...")
- 18:16, 11 August 2011 (diff | hist) . . (+1,128) . . N Results form (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...")
- 18:15, 11 August 2011 (diff | hist) . . (+165) . . N The Results Menu (Created page with "Choosing this menu choice instantly brings up the Results form. Results are available only if enough information to compute a molecular weight has been entered.")
- 18:15, 11 August 2011 (diff | hist) . . (+3,539) . . N The Estimating Databases Menu (Created page with "This menu allows the user to access the phyconst.mdb data base to modify or add to the calculation/interpolation data used by Sednterp. The two things most likely to be modified...")
- 18:11, 11 August 2011 (diff | hist) . . (+2,001) . . N The Experiment Section (Created page with "This section of the main form is organized to contain information that is particular to particular experiments. Since samples and buffers may be common to many experiments, they...")
- 18:09, 11 August 2011 (diff | hist) . . (-620) . . Buffer Components form
- 18:09, 11 August 2011 (diff | hist) . . (+4,551) . . 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...")
- 18:08, 11 August 2011 (diff | hist) . . (+1,361) . . N The Buffer Section (Created page with "The buffer section of the main form displays information particular to a buffer. The section on the main form displays the density and viscosity of the buffer. Other information...")
- 18:07, 11 August 2011 (diff | hist) . . (+1,127) . . N The Results Form (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 dep...")
- 18:07, 11 August 2011 (diff | hist) . . (+4,792) . . N The Sample Composition Form (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...")
- 18:07, 11 August 2011 (diff | hist) . . (+1) . . Sample Composition Form
- 18:06, 11 August 2011 (diff | hist) . . (+166) . . N Forms (Created page with "A form is a window that contains any number of Microsoft Windows or Visual Basic controls such as text boxes, buttons, and menus. It is the basic unit of the program.")
- 18:05, 11 August 2011 (diff | hist) . . (+1,114) . . N Overview of Sednterp Screens (Created page with "The purpose of the Sednterp program is to automate the calculation of molecular parameters from experimental information. The purpose of most of the forms in Sednterp is to ...")
- 18:04, 11 August 2011 (diff | hist) . . (+46) . . References
- 18:03, 11 August 2011 (diff | hist) . . (+7,096) . . N References (Created page with "1. R.J. Goldberg, J. Phys. Chem., 1953, 57, 194. 2. J.W. Williams, K.E. Van Holde, R.L. Baldwin, and H. Fujita, Chem. Rev., 1958, 58, 715. 3. E.F. Cassasa and H. Eisenberg Adv. i...")
- 18:02, 11 August 2011 (diff | hist) . . (+4,202) . . N As before (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 ...")
- 18:01, 11 August 2011 (diff | hist) . . (+967) . . N Calculating Hydration from Asymmetry Estimates (Created page with "Calculating Hydration from Asymmetry Estimates Should the user supply an axial ratio (as major-axis/minor-axis), the corresponding values of the degree of hydration for both the...")
- 18:00, 11 August 2011 (diff | hist) . . (0) . . N File:Equation27.GIF
- 18:00, 11 August 2011 (diff | hist) . . (0) . . File:Equation30.GIF (uploaded a new version of "File:Equation30.GIF")
- 18:00, 11 August 2011 (diff | hist) . . (0) . . N File:Equation29.GIF
- 17:59, 11 August 2011 (diff | hist) . . (0) . . N File:Equation28.GIF
- 17:59, 11 August 2011 (diff | hist) . . (0) . . N File:Equation30.GIF
- 17:49, 11 August 2011 (diff | hist) . . (+143) . . N 52 (Created page with "M. Luscher-Mattli, 'Thermodynamic Data for Biochemistry and Biotechnology', H.-J. Hinz, ed., Springer-Verlag, Berlin, 1986, Chapter 11, p. 276.")
- 17:47, 11 August 2011 (diff | hist) . . (+144) . . N 39 (Created page with "D.W> Kupke, 'Physical Principles and Techniques of Protein Chemistry, part C', S.J. Leach, ed., Academic Press, New York, 1973, Chapter 1, p. 1.")
- 17:46, 11 August 2011 (diff | hist) . . (+25) . . Calculating Maximum Hydration
- 17:46, 11 August 2011 (diff | hist) . . (0) . . N File:Equation25.GIF
- 17:44, 11 August 2011 (diff | hist) . . (+2,378) . . N Calculating Maximum Hydration (Created page with "Water of hydration is considered to be water that differs from the bulk phase due to its interaction with the protein. Our knowledge of the degree of hydration for proteins is p...")
- 17:41, 11 August 2011 (diff | hist) . . (+2,084) . . N Calculating 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...")
- 17:39, 11 August 2011 (diff | hist) . . (+4) . . Density of the buffer at 20 C
- 17:39, 11 August 2011 (diff | hist) . . (+4,461) . . N Density of the buffer at 20 C (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...")
- 17:39, 11 August 2011 (diff | hist) . . (+1) . . Calculating the Density Temperature Correction
- 17:38, 11 August 2011 (diff | hist) . . (+2,111) . . N Calculating the Density Temperature Correction (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...")
- 17:35, 11 August 2011 (diff | hist) . . (0) . . N File:Equation15.GIF
- 17:35, 11 August 2011 (diff | hist) . . (0) . . N File:Equation14.GIF
- 17:29, 11 August 2011 (diff | hist) . . (+4) . . Calculating Density Increments
- 17:29, 11 August 2011 (diff | hist) . . (+4,457) . . N Calculating Density Increments (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...")
- 17:17, 11 August 2011 (diff | hist) . . (+158) . . N 43 (Created page with "J.C. Lee and S.N. Timasheff, 'Methods in Enzymolgy Volume 61', C.H.W. Hirs and S.N. Timasheff, eds., Academic Press, Orlando, Florida, 1979, Chapter 4, p. 49.")
- 17:14, 11 August 2011 (diff | hist) . . (+162) . . N 38 (Created page with "T. Arakawa and S.N. Timasheff, 'Methods in Enzymology Volume 117', C.H.W. Hirs and S.N. Timasheff, eds., Academic Press, Orlando, Florida, 1985, Chapter 5, p. 60.")
- 17:12, 11 August 2011 (diff | hist) . . (+162) . . N 37 (Created page with "V. Prakask and S.N. Timasheff, 'Methods in Enzymology Volume 117', C.H.W. Hirs and S.N. Timasheff, eds., Academic Press, Orlando, Florida, 1985, Chapter 4, p. 53.")
- 17:11, 11 August 2011 (diff | hist) . . (+3,595) . . N Calculating Denatured v-bar Estimates (Created page with "It is often useful or necessary to measure the molecular weight of proteins in denaturants. In this case, preferential binding of the denaturant to the protein will affect the pa...")
- 17:01, 11 August 2011 (diff | hist) . . (0) . . N File:Equation9.GIF
- 17:01, 11 August 2011 (diff | hist) . . (0) . . N File:Equation10.GIF
- 15:48, 11 August 2011 (diff | hist) . . (+3,165) . . N Calculating v-bar estimates (Created page with "The 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...")
- 15:47, 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...")
- 15:46, 11 August 2011 (diff | hist) . . (+3,542) . . N 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....")
- 15:45, 11 August 2011 (diff | hist) . . (+167) . . N 58 (Created page with "J.G. de la Torre, Analytical Ultracentrifugation in Biochemistry and Polymer Science, Royal Society of Chemistry (Edited by S. Harding and A. Rowe), 1992, pp. 333-345.")
- 15:44, 11 August 2011 (diff | hist) . . (+64) . . N 57 (Created page with "M.W. Kirschner and H.K. Schachman, Biochemistry, 1971, 10, 1900.")
- 15:43, 11 August 2011 (diff | hist) . . (+70) . . N 56 (Created page with "E.G. Richards and H.K. Schachman, J. Amer. Chem. Soc., 1957, 79, 5324.")
- 15:42, 11 August 2011 (diff | hist) . . (+418) . . N Contact (Created page with "For general questions regarding interpretation of sedimentation data and the theory behind this program, contact Dr. Thomas Laue, Department of Biochemistry, University of New Ha...")
- 15:42, 11 August 2011 (diff | hist) . . (+4,457) . . N Equation 13 (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...")
- 15:36, 11 August 2011 (diff | hist) . . (+4) . . Limitations
- 15:36, 11 August 2011 (diff | hist) . . (+3,721) . . N Limitations (Created page with "There are three categories of limitations in the calculations implemented in Sednterp. The first category is limitations implied in choosing a method of interpretation. Sednter...")
- 15:33, 11 August 2011 (diff | hist) . . (+1,905) . . N Equation 3 (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...")
- 15:33, 11 August 2011 (diff | hist) . . (+32) . . Buffer and Solute Solution Parameters
- 15:31, 11 August 2011 (diff | hist) . . (+1,176) . . N Buffer and Solute Solution Parameters (Created page with "vbar ρ and η are needed for further interpretation of s* and σ: s* and σ are directly accessible from sedimentation data. However, more often than not, it is the anhydrous mo...")
- 15:31, 11 August 2011 (diff | hist) . . (0) . . N File:Equation5.GIF
- 15:28, 11 August 2011 (diff | hist) . . (+787) . . N Reduced Apparent Molecular Weight (Created page with "The reduced apparent molecular weight, σ, is directly available from sedimentation equilibrium: Equating equation 1 and equation 2, one obtains the fundamental equation ...")
- 15:28, 11 August 2011 (diff | hist) . . (+1,905) . . N Sedimentation Coefficient (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...")
- 15:27, 11 August 2011 (diff | hist) . . (+1,483) . . N Overview of Information Needed (Created page with "'''Overview of Information needed:''' Regardless of whether velocity or equilibrium experiments are conducted, the values obtained by direct analysis of the data must be adjuste...")
- 15:25, 11 August 2011 (diff | hist) . . (+8) . . Primary Reference
- 15:25, 11 August 2011 (diff | hist) . . (+904) . . N Primary Reference (Created page with "Sednterp was originally developed as a template for a spreadsheet by Thomas M. Laue, Bhairavi D. Shah, Theresa M. Ridgeway and Sandra L. Pelletier. A previous version of a sedim...")
- 15:25, 11 August 2011 (diff | hist) . . (+876) . . N Acknowledgments (Created page with "Work on the original project was supported in part by a Grant-in-Aid #850-781 and #870-1092 from the American Heart Association and Grants BBS 86-15815 and DIR 90-02027 from the ...")
- 15:25, 11 August 2011 (diff | hist) . . (+170) . . N Bugs (Created page with "Bugs are, by definition, either 1. an error one of the other collaborators put into the program or 2. things in the program we haven't yet realized are really features.")
- 15:24, 11 August 2011 (diff | hist) . . (+418) . . N Who to Contact for Information and Feedback (Created page with "For general questions regarding interpretation of sedimentation data and the theory behind this program, contact Dr. Thomas Laue, Department of Biochemistry, University of New Ha...")
- 15:23, 11 August 2011 (diff | hist) . . (+3) . . Development and Distribution of Sednterp
- 15:23, 11 August 2011 (diff | hist) . . (+499) . . N Development and Distribution of Sednterp (Created page with "The specifications for Sednterp were originally designed by Thomas M. Laue, Bhairavi D. Shah, Theresa M. Ridgeway and Sandra L. Pelletier. Their work is described in Ref. 59. Dr...")
- 15:22, 11 August 2011 (diff | hist) . . (+3,964) . . N *.buf (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...")
- 15:21, 11 August 2011 (diff | hist) . . (+4,791) . . N *.smp (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...")
- 15:21, 11 August 2011 (diff | hist) . . (+4,791) . . N *.seq (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...")
- 15:20, 11 August 2011 (diff | hist) . . (-12) . . List of Standard File Endings
- 15:19, 11 August 2011 (diff | hist) . . (+4,891) . . N *.ini (Created page with "The file menu on the main form contains the following options. 1. '''New data entry form'''. This choice re-initializes the main form. Choose this option to start over on a ...")
- 15:19, 11 August 2011 (diff | hist) . . (+1,254) . . N List of Standard File Endings (Created page with "Sednterp uses conventions for the three letter file ending for the various files important to the program. *.ini Initialization file. Sednterp saves initialization data in...")
- 15:18, 11 August 2011 (diff | hist) . . (+1,128) . . N Results Form (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...")
- 15:17, 11 August 2011 (diff | hist) . . (+1,184) . . N XLGraph (Created page with "XLGraph is a Windows program for graphing and manipulation of data from the XL-A or XL-I. If you are still using the DOS-based Beckman software for controlling your XL-A, XLGrap...")
- 15:12, 11 August 2011 (diff | hist) . . (+375) . . N Svedberg (Created page with "Svedberg is a Windows program for analysis of sedimnetation velocity data form the XL-A. It is particularly intended for anaylsis of low molecular weight samples whose boundaries...")
- 15:09, 11 August 2011 (diff | hist) . . (+2,402) . . N Graphs Available (Created page with "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 and printing based on J...")
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