Manual |
UltraScan utilizes a number of file naming conventions and file formats in order to achieve efficient and fast data access. This is crucial, especially for datasets with many scans, where the loading of experimental data can take a very long time if the file structure is not implemented properly. This requires for most files to be stored in a binary file format. For cases where ASCII files are necessary for ease of porting data informations from one architecture to another, a conversion routine exists that allows export of data files to a number of different formats.
Following is a listing of all file formats and file names used in UltraScan:
Sedimentation Velocity:
Sedimentation Equilibrium:
Finite Element Simulations:
Self-association Equilibrium:
Structure for experimental data diagnostics::
struct runinfo { QString data_dir; // path to data directory QString run_id; // Run identification QString cell_id[8]; // descriptive string for cell contents int wavelength_count[8]; // how many wavelengths have been measured for each cell int wavelength[8][3]; // up to 3 wavelengths per cell int scans[8][3]; // how many scans are there for each lambda in each cell? float avg_temperature; // average temperature of the run int temperature_check; // does the temperature vary over the run more than allowed by tolerance? float time_correction; // time correction for rotor acceleration period float duration; // length of the run int total_scans; // how many scans are there total in the Run? float ***temperature; // temperature of each scan float ***time; // time stamp of each scan float ***omega_s_t; // omega-square-t of each scan float ***plateau; // plateau value of each scan uint ***rpm; // Rotor speed in rotation per minute float meniscus[8]; // meniscus for each cell float baseline[8][3]; // baseline of each data set float range_right[8][3][3]; // radius where the data starts (third dimension for 6-channel equilibrium cells) float range_left[8][3][3]; // radius where the data stops float delta_r; // radial datapoint density (increment) int centerpiece[8]; // centerpiece properties // 1. Digit = 0: 2 channels // 1. Digit = 1: 6 channels // 2. Digit = 0: Epon/Charcoal // 2. Digit = 1: Aluminum // 3. Digit = 0: Conventional // 3. Digit = 1: Synthetic // Example 1: 100: 6 channel, Epon, Conventional // Example 2: 1: 2 channel, Epon, Synthetic int rotor; // AN-60 = 1, AN-50 = 0 };
The name for this file will always be <run_id>.us.v for velocity experiments and <run_id>.us.e for equilibrium experiments, where <run_id> is a variable that describes the unique run identification given to the run by the user during editing.
The edited data for each dataset is written to a binary file. Each dataset consists out of all scans belonging to a single cell and a single wavelength. The naming convention for the datafiles is as follows:
<run_id>.<exp>.<cell><wavelength><channel>
where:
<run_id>.<cell><wavelength><channel> (channel information only for equilibrium experiments)
Exported ASCII data will be saved into the "Results" directory.
The file structure is as follows:
Column 1 | Column 2 | Column i |
Radius Position | Absorbance Scan 1 |
Absorbance Scan i-1 |
<run_id>.<method>.<cell><wavelength><channel>
where:
Sedimentation Velocity:
File structure:
First column: inverse square-root of the time of each scan
All other columns: apparent sedimentation coefficients for each division.
Number of rows = number of scans
Number of columns = number of divisions + 1 (for the time of the scans)
Column 1 | Column 2 | Column 3 | Column 4 | Column 5 | Column 6 |
Divisions
(one row for each division) |
Average S-value | Slope | Intercept
(Corrected S-value) |
Standard Deviation | Correlation |
Column 1 | Column 2 | Column 3 | Column 4 |
S-value
(Envelope) |
Frequency | S-value
(Histogram) |
Frequency |
Column 1 | Column 2 | Column i | Column i+1 | Column 19 | Column 20 |
Boundary Fraction
of Dataset 1 |
S-value
of Dataset 1 |
Boundary Fraction
of Dataset (i+1)/2 |
S-value of
Dataset (i+1)/2 |
Boundary Fraction
of Dataset 10 |
S-value of
Dataset 10 |
Column 1 | Column 2 | Column i | Column i+1 | Column 19 | Column 20 |
Frequency
of Dataset 1 |
Molecular Weight
of Dataset 1 |
Frequency
of Dataset (i+1)/2 |
Molecular Weight of
Dataset (i+1)/2 |
Frequency
of Dataset 10 |
Molecular Weight of
Dataset 10 |
Column 1 | Column 2 | Column i |
Radius Position | Absorbance Scan 1 |
Absorbance Scan i-1 |
Column 1 | Column 2 | Column i |
Radius Position | Absorbance Scan 1 |
Absorbance Scan i-1 |
Column 1 | Column 2 | Column i |
Radius Position | Absorbance Scan 1 |
Absorbance Scan i-1 |
Column 1 | Column 2 | Column 3 |
Scan Number | Second Moment
S-Value |
Second Moment
Point Position (cm) |
Column 1 | Column 2 | Column i |
Radius Position | Absorbance Difference 1 (scan_2 - scan_1) |
Absorbance Difference i-1 (scan_i - scan_i-1) |
Column 1 | Column 2 | Column i |
S-value x 10^13 | Absorbance Difference 1 (scan_2 - scan_1) |
Absorbance Difference i-1 (scan_i - scan_i-1) |
Column 1 | Column 2 | |
S-value * 10^13 | Average g(s*) Data |
Column 1 | Column 2 | Column i |
Radius Position | Absorbance Difference 1 (scan_2 - scan_1) |
Absorbance Difference i-1 (scan_i - scan_i-1) |
Column 1 | Column 2 | Column i |
S-value * 10^13 | Absorbance Difference 1 (scan_2 - scan_1) |
Absorbance Difference i-1 (scan_i - scan_i-1) |
Column 1 | Column 2 |
S-value * 10^13 | Average g(s*) Data |
Sedimentation Equilibrium:
Column 1 | Column 2 | Column 3 | Column 4 | Column 5 | Column 6 | Column 7 | Column 8 | Column 9 |
Scan Number | Molecular Weight |
Slope | Intercept | Standard Deviation |
Correlation | Points in Scan |
Runs in Scan |
% Runs w.r.t Scan Points |
Column 1 | Column 2 |
Concentration | Frequency of occurence |
Column 1 | Column 2 |
Wavelength | Extinction Value |
Finite Element Simulations:
Column 1 | Column 2 | Column i |
Row 1: Plateau Concentration of Scan 1 |
Row 1: Plateau Concentration of Scan 2 |
Row 1: Plateau Concentration of Scan i |
Radius | Absorbance of Scan 1 | Absorbance of Scan i-1 |
Extrapolation plot:
Column 1 | Column 2 | Column i |
Apparent S-value * 10^13 for division 1 | Apparent S-value * 10^13 for division 2 | Apparent S-value * 10^13 for division i |
Note: Number of Rows = Number of Scans, Number of Columns = Number of Divisions |
Distribution plot:
Column 1 | Column 2 | Column 3 | Column 4 | Column 5 | Column 6 |
Division | Average S-value | Slope of Extrapolation | Intercept (Extrapolated S-value | Standard Deviation | Correlation Coefficient |
Column 1 | Column 2 | Column 3 |
Scan Number | 2. Moment Point | 2. Moment S-value |
Column 1 | Column 2 | Column 3 | Column 4 | Column 5 | Column 6 |
S-value * 10^13 | Average g(s*) Data | s* S-value for first difference | g(s*) for scan_1 - scan_2 | s* S-value for second difference | g(s*) for scan_3 - scan_2 |
Note: Number of Rows = Number of points, number of columns = (number of scans - 1) * 2 + 2 columns for the average g(s*) data. |
Column 1 | Column 2 | Column 3 | Column 4 | Column 5 | Column 6 |
S-value * 10^13 | Average g(s*) Data | s* S-value for first difference | g(s*) for delta_C/delta_radius | s* S-value for second difference | g(s*) for delta_C/delta_radius |
Note: Number of Rows = Number of points - 1, number of columns = (number of scans) * 2 + 2 columns for the average g(s*) data. |
Self-Association Equilibrium:
Column 1 | Column 2 | Column 3 | Column 4 |
Total Concentration | Monomer Concentration | Dimer Concentration | Tetramer Concentration |
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Last modified on January 12, 2003.