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generate sedimentation profiles


See the Tutorial on Generating New Simulated Data for more information how to use this function.

This tool allows to simulate the sedimentation process and generate data files formatted like Beckman Optima XL-A.  In contrast to the Run and Fit commands which require data files to be loaded (and compare the loaded with the simulated data), the Generate Data function creates new data files of the sedimentation process with user-specified time-increments. 

Before invoking this function, the appropriate model has to be selected. Then, after using this ‘Generate Data’ function, the user is prompted to give the following information (some of which is similar to the data acquisition software in the AUC):

1) Fit with M and s or D and s. This allows to use either diffusion coefficients or - via the Svedberg equation - molar masses as input.  For the partial specific volume, the default value of 0.73 ml/g is used unless a new value is entered in the Options->Set vbar*rho menu.  (This questions sets and overwrites the switch Options->Fitting Options->Set M and s)

2) density of points (cm). This will be the radial increment for the data to be saved.  Typical, 0.003 cm seems realistic, corresponding to the entry in the .scn file of the XLA software.  (This parameter here is not identical with the discretization of the Lamm equation, which will be governed by the GridSize parameter.)

3) rotor speed (rpm). This is the rotor speed in rpm for the simulated sedimentation.

4) simulate with rotor acceleration phase? This means that the Lamm equation can be solved with or without simulating an initial linear increase in rotor speed.  If choosing yes, a value for the rotor acceleration is required -- typical experimental values on the XLA with maximal acceleration settings are about 200rpm/sec.

5) time interval of scans. Time interval in seconds of the distributions to be stored in files (similar as the entry in the method dialog of the XLA software).

6) number of simulated scans. Similar to the entries in the XLA software.

7) std of noise. To make the simulation realistic, Gaussian noise can be added to the simulated distributions.  This is useful, in particular, when studying the resolution or sensitivity of a given data analysis method.  A conservative estimate of the noise would be 0.01.

NEW:  For self-association models, one can enter now the loading concentration and association constant in molar units, which together with a molar extinction coefficient (per cm) will be transformed to the proper log10(Ka) and apparent ctot values. (These can still be modified in the following parameter box, if desired.)

8) Fit and Simulation Parameters. This is the same dialog box as described in Parameters; the details will depend on the sedimentation model used.  Please note here that the meniscus is automatically suggested to be at 6.2 cm, and the bottom at 7.2 cm. Change these entries as needed in the simulation.

9) Save generated data as. Requests filenames for the distributions to be saved. The calculations have to be saved, otherwise the simulation will be aborted. Files will be saved in the XLA format.

After this, the simulation will be calculated, and the calculated profiles are shown in the upper plot, as if the data had been loaded.  

If the fit limits have not been set before, a warning message may appear about a possible problem with the right fit limit (see FAQ).  This can be ignored, or the fitting limits can be properly set.  Dependent on the concentration close to the bottom, the sedimentation boundaries may not be visible without setting the fit limits and rescaling the data plot

In the current version, data can only be generated for constant initial distribution. (No experimental file can be taken to initialize the propagation).  This limitation could be circumvented, however, loading data files with the right time intervals, and using the Run function and saving the fits.  For generating sedimentation data with model size-distributions, essentially the same procedure as described above can be used.  The model distribution should be placed in a ASCII file called "distrib.dat" and should be copied to the folder "c:\temp". The format of the file is simple two-column matrix (it should be copied best from the saved results of a previous distribution analysis).

If the data are reloaded, note that the selected loading options will affect the details of how the data appear.  In particular, the treatment of the rotor acceleration phase will lead to errors in the Elapsed Seconds, which translate to very small discrepancies if re-analyzing the saved data.  Also, small deviations can occur when reloading noise-free simulated data because of the limited precision of the w2t entry of the files.