Sedphat organizes the data in 'Experiments', which are objects that consist of the information of the experiment type, location of the data and list of data filenames, buffer conditions, sample extinction coefficients, some centrifugal parameters like meniscus, bottom, fitting limits, expected standard deviation, etc. They can be of different type (see the overview, and the specific instructions for loading a single sedimentation equilibrium profile, multi-speed equilibrium, sedimentation velocity, dynamic light scattering and isotherm data).
Note: Multiple sedimentation equilibrium profiles from the same ultracentrifugal cell and acquired at the same wavelength should be loaded as a single multi-speed equilibrium experiment, in particular if mass conservation will be used. They could also be loaded as several single sedimentation equilibrium profiles, but this would have significant drawbacks and provide less flexibility in sharing the baseline parameters.
New in version 2.0: Sedphat experiments can be created automatically by exporting data from Sedfit.
For global analysis, currently up to 20 (version 1.9b) such experiments can be loaded and analyzed jointly. Relationships between some parameters of the different experiments can be established (see this overview and the details here).
Once an experiment has been defined, the complete information can be saved (in a file *.xp) and reloaded. The functions for the manipulation of the experiments are in the Data menu.
The general strategy is as follows:
1) load the data for a new experiment (use one of the functions Load New Sedimentation Velocity Data, Load New Sedimentation Equilibrium Data, Load New Multi-Speed Equilibrium Data, Load New DLS Data or Load New Isotherm Data)
2) enter information on the experimental details in the Experiment Parameters box, which may look like this
for sedimentation velocity data, but slightly different for the other data types. For information on these boxes see here.
3) specify graphically the fitting limits. This follows the same conventions as in Sedfit, and detailed instructions can be found in the Sedfit help web for loading data.
4) save the experiment as an xp-file with the menu function Data->Save Experiment. For reloading a previously saved experiments, this simplifies to a single step of loading the xp-file (Data->Load Experiment). A reminder will appear to specify the partial-specific volume under standard conditions.
After loading an experiment, the data will be shown in the Sedphat window. Note that graphical input can be made directly in the graphs for each experiment. However, a more detailed view is possible using the 'Display->Zoom Into 1 Data Set' function.
Note that you can use mouse functions to zoom and unzoom into particular regions of any data set.
Experiment Number: Each experiment has a number associated, which is the order of loading. This will be the same as the order of the plots from left to right in the Sedphat window (upper row before lower row). Many Sedphat functions operate on specific experiments, and the user has to specify the corresponding experiment number.
The data analysis models permit global fitting to all active experiments jointly, or alternatively, they permit a local fit to only a single experiment. Experiments can be excluded from the analysis in two different ways: They can be permanently removed from the Sedphat memory by using the function Data->Remove Experiment, or they can be temporarily deactivated in the Experiment Parameters box. After a fit, the xp-files can be updated with the current local parameters using the Data->Save All Experiments function.
It should be noted that not all parameters are specified in the experiment file: the partial-specific volume at standard condition (water, 20C) is defined separately and is part of the global model.
Storage of the xp-files: Sometimes it is necessary to edit the information of the xp-file of an experiment. It is a text file, which can be opened and changed with any text editor, such as the MS Notepad. The format of an xp-file is shown below.
4 (ExperimentType: MULTISEDEQ)
"C:\xladata\DC-SIGN\RR5B\XLADA302\eq"
" 25k250_084.Ra1 20k251_052.ra1 15k250_030.ra1"
1.002200 (fBufferDensity)
0.001002 (fBufferViscosity)
0.712000 (VBAR)
6.693300 (Meniscus)
7.204400 (Bottom)
0.000000 (MAXMENISCUS)
0.000000 (MINMENISCUS)
7.212900 (MAXBOTTOM)
7.152900 (MINBOTTOM)
6.712811 (FitLeftLim)
7.134190 (FitRightLim)
0.000000 (WeightExperiment)
0.005000 (ExperimentalNoise)
0 (blocalFitTimeIndepNoise)
1 (blocalFitRINoise)
1 (blocalAutoVaryBaseline)
1 (blocalVaryBottom)
0 (blocalVaryMeniscus)
1 (blocalVaryMeniscusWarned)
0.000000 (xBaseline)
1.000000 (xConcentrationFactor)
12157.466797 (xExtinctionCoeffA)
0 (bVaryExtinctionCoeffA)
1.000000 (xExtinctionCoeffB)
0 (bVaryExtinctionCoeffB)
2 (Centerpiece)
1.000000e-06 (pLocalConcentrations[1])
1.000000e-06 (pLocalConcentrations[2])
1.000000e-06 (pLocalConcentrations[3])
1.000000e-06 (pLocalConcentrations[4])
3 (NFILES)
1 (ppMultiLocalConcentrations follow)
2.318014e-06 (ppMultiLocalConcentrations[1][1])
5.000000e-06 (ppMultiLocalConcentrations[1][2])
5.000000e-06 (ppMultiLocalConcentrations[1][3])
5.000000e-06 (ppMultiLocalConcentrations[1][4])
1.777017e-06 (ppMultiLocalConcentrations[2][1])
5.000000e-06 (ppMultiLocalConcentrations[2][2])
5.000000e-06 (ppMultiLocalConcentrations[2][3])
5.000000e-06 (ppMultiLocalConcentrations[2][4])
1.261792e-06 (ppMultiLocalConcentrations[3][1])
5.000000e-06 (ppMultiLocalConcentrations[3][2])
5.000000e-06 (ppMultiLocalConcentrations[3][3])
5.000000e-06 (ppMultiLocalConcentrations[3][4])
0.712000 (global VBAR20)
0.300000 (global HYDRATION)
1.200000 (pathlength)
The individual entries are self-explanatory, except for a few entries. The most important one, and maybe the only one that may require manual change is the third line:
"C:\xladata\DC-SIGN\RR5B\XLADA302\eq" " 25k250_084.Ra1 20k251_052.ra1 15k250_030.ra1"
This is the location of the actual raw data files. When moving the data to a different computer or a different directory, it is usually necessary to change the directory information appropriately. The directory is followed by the data filenames to be loaded. If you want to remove some data from the set, they can be simply deleted here, but an according change in line 34 specifying the total number of files is necessary.
New in version 4.0: Path-Independent xp-files and configuration files can be generated.
New in version 1.5: Note that the format of the xp-file has changed a little, in particular the line specifying the data directory and the files. You may need to adjust it to the new format.
Most other parameters can be changed with the Experiment Parameter box from within Sedphat (although you may want to save the experiment after the changes). Exceptions are the values for MAXMENISCUS and MINMENISCUS etc., which are the constraints for the meniscus location when floating this parameter. They can be changed from within Sedphat by switching the fitting mark off, closing the Experiment Parameter box, reopening the Experiment Paramter box, and switching the fitting mark on again. This will cause Sedphat to ask for the constraints for this parameter.
The concentration values in the xp-file are just the best-fit local concentration at the time of the last save (they are not updated automatically). They are model-dependent, and are only partially used automatically.