Manual

Radial Derivative (dC/dr) Analysis:

The Radial Derivative method can be used to determine the point of steepest slope in a boundary (also called midpoint). The Radial Derivative method is sensitive to noisy data and often requires significant smoothing. Unlike the van Holde - Weischet method, the Radial Derivative method does not correct for diffusion. Unlike the Time Derivative method, the peaks are directly proportional to the relative amount of the species present in the sample.

You start the Radial Derivative data analysis by clicking on "Radial Derivative" in the Velocity sub-menu of the main menu. The main Radial Derivative Data analysis window will appear.

The first step in the analysis requires that you load an UltraScan dataset that has previously been edited with the UltraScan editing module. UltraScan sedimentation velocity datasets always have the suffix ".us.v". Click on the "Load Dataset" button in the left upper corner of the control panel. Simply select the desired run from the selection of available runs in the dataset loading dialog. Once loaded, the Run Details will be shown. Click on the "Accept" or "Cancel" button, and you will be returned to the analysis window, which will show the first available dataset of the selected run in the edited data window on the lower right panel, and the Radial Derivative analysis will be shown in the upper right panel of the analysis window. If the scans in your experimental data have not cleared the meniscus (as judged by the baseline defined during editing), an insufficient number of scans may be available for the analysis and an error message will be shown. In that case, you can raise the baseline and reduce the fraction of the boundary analyzed (see below).

Analysis Functions:

Click on these buttons to control the radial derivative analysis: Load Data: Load edited data sets (with the *.us suffix). A file dialogue will allow you to select a previously edited and saved velocity experiment. If the data was edited with an older version of UltraScan than the current, an error message will be displayed. Run Details: View the diagnostic details for a particular run. Avg. dC/dr Plot: View the average dC/dr plot derived from the dC/dr vs. S-value plot. Save Data: Write out a copy of all results to an ASCII formatted data file suitable for import into a spreadsheet plotting program. See "File Structures and Formats" for details. Note: These files are overwritten each time this button is clicked. Only the last version of the analysis will be saved! Print Data: Load the printer control panel for printing of plot graphics View Data Report: See the data report for the last analysis setting. Note: This file is re-written each time it is accessed. Only the current analysis result is available. Help: This help file Close: Close the dC/dr analysis window.

Run Information:

Run ID: The name of the run given during editing Temperature: The average temperature calculated from the entire run Available Cells: The numbers the cells that contain analyzable data Clicking on a cell and wavelength selection will bring up the cell contents description for that cell and wavelength. Scroll through this list to bring up information for cells > 3. If there is no data available for the selected cell, the program will list "No Data available". Selecting a cell/wavelength combination will automatically bring up the corresponding dataset and present the analysis.

Experimental Parameters:

Here you can enter the corrections for density, viscosity, and partial specific volume of your sample. As you change the information in these fields, the program will automatically update the analysis to correct the S-value according to the specified buffer conditions. If the data was retrieved from the database and associated with the correct buffer file and peptide file, the density, viscosity and partial specific volume (vbar) will automatically be updated to the appropriate values and don't need to be adjusted to produce S 20,W corrected values. Density: Click to calculate the density based on the composition of your buffer. Viscosity: Click to calculate the viscosity based on the composition of your buffer. vbar(20o): Click to calculate the partial specific volume for a peptide based on its primary amino acid sequence and correct the vbar value for the current temperature. Skipped: This field refers to the scans at the beginning of the run that are excluded from the analysis. the van Holde - Weischet analysis requires that the scans have cleared the meniscus in order to be analysable. If they haven't cleared the meniscus, they are automatically excluded from the analysis. Note: This number may change if the percentage and position of the analyzed boundary are changed (see below).

Analysis Controls:

Reset Data - use this button to reset the default settings for the analysis. X-Axis Coordinate setting: This toggle switch allows you to select the X-Axis coordinate. There are two display modes: The default mode will display dC/dr profiles of the experimental data versus radius (Checkbox: "x: r", meaning X-axis is in radius coordinates). The other mode is to display the dC/dr profiles versus S (Checkbox: "x: S", meaning X-axis is in S-value coordinates). S-value Cutoff: The S-value Cutoff is used to control the maximum S-value displayed in the dC/dt vs. S-value plot. By default, this cutoff is set to a maximum of 1000s, which may be unrealistic for most samples. Changing this value allws you then to scale the plot to the proper dimensions. Data Smoothing: Use this feature to smooth the experimental data. For noisy data, increasing this parameter can improve the clarity and appearance of the results considerably. Please note: Whenever possible, especially for very steep boundaries with low diffusion, try to avoid using too much smoothing to prevent artificial modification of the boundary shape. Smoothing is performed based on a frame average. The number shown represents the size of the smoothing kernel used (the number of datapoints averaged for a single point). The algorithm used is non-destructive of the original data and hence the smoothing is reversible. Also, point smoothing is independent, where the smoothing of one point does not have any effect on the smoothing of its neighbors. Only unsmoothened points are used for the calculation of the smothed value. Each time you click on the counter, the current dataset will be reset to the full dataset. % of Boundary: This is the portion of the boundary used for the analysis. 100 % refers to the entire boundary, reaching from the baseline concentration value to the plateau concentration value. This portion is shown in yellow in the experimental data plot at the lower right panel of the main analysis window. Excluded data is shown in blue. Changing this number will automatically reset the position of the analyzable portion of the boundary in the center of concentration between the baseline and the plateau concentration. Boundary Position (%): For percent-boundary values less than 100 %, this number refers to the percentage of total concentration by which the remainder (=un-analyzed portion of the boundary) is shifted away from the baseline. A value of 0% refers to a data analysis start at the baseline. This number is always less than or equal to 100 % - (% of Boundary). It allows you to control the position of the analyzed portion relative to the baseline. The blue colored portion of a scan is excluded from the analysis, and the yellow portion is analyzed. Exlude Single Scan: When setting this counter to a non-zero value, the respective scan will be highlighted in red. Clicking on "Excl. Single Scan" while a scan is highlighted in red will delete this scan from the analysis. Deleting scans from the analysis is irreversible and can only be reset by clicking on the "Reset" button or by reloading the data (when smoothing, the data is always automatically reloaded). Exclude Scan Range: Same as "Exclude Single Scan", except for multiple scans. To use this feature, select first the start scan of the range by using "Exclude Single Scan", then complete the scan range by using "Exclude Scan Range". Status: The status bar informs the user about the progress of the analysis. On slower computers this has more significance than on a fast Unix machine.