From version 4.0 and higher, Sedphat can generate two different kinds of configurations, see the Path-Independent Configurations below.
Sedphat can save its current state (version 1.9 and above). The combination of a set of experiments, the model, the model parameters, and the links between the experiments and shared parameters is termed 'configuration'.
You create a configuration by using the function Data->Save Current Configuration As. This will make a 'sedphat' file on your disk. The path of the current configuration will be identified in the title bar of the Sedphat window, and it can be updated as the analysis proceeds. For the menu functions see the Data menu. A change in the model or a change in the loaded experiments will require a new configuration file to be named.
At this point, another file called *.sedphat_PAR will also be created. This file contains the information on the nature of the model and the parameters values.
You can load a configuration into Sedphat by dragging-and-dropping a 'sedphat' file into the Sedphat window. This is true also for the sedphat_PAR files, which only switch the model and apply the global parameter values saved in this file.
Follow this procedure for enabling Sedphat to be started up with a configuration by double-clicking the 'sedphat' file (some of the details may be dependent on your Windows version):
1) double-click a 'sedphat' file (or right-click and select the menu 'open')
2) Windows will tell you that it does not know how to open 'sedphat' files
3) use the option to 'select a program from a list
4) the list of programs known to Windows does not contain Sedphat . Therefore, use 'Browse' and navigate to the 'c:\sedfit\sedphat.exe' file (if you have it copied to the default location).
5) check 'Always use the selected program to open this kind of file', and OK.
This will associate Sedphat with 'sedphat' files permanently on your computer.
A configuration on the disk is a ANSI text file, which can be edited with any text editor. An example of a configuration file is the following:
1 1 C:\sedfitworkshop\data\singlespeciescofM\vel.xp
2 1 C:\sedfitworkshop\data\singlespeciescofM\eq.xp
3 1 C:\sedfitworkshop\data\singlespeciescofM\dls.xp
-1 0 end
0.730000 0.300000 (vbar20, hydration)
g 2 (#global parameters)
1 (species analysis)
1 1 1 1 1 0 0
2 2 2 2 2 0 0
3 3 3 3 3 0 0
4 4 4 4 4 0 0
5 5 5 5 5 0 0
6 6 6 6 6 0 0
7 7 7 7 7 0 0
8 8 8 8 8 0 0
9 9 9 9 9 0 0
10 10 10 10 10 0 0
11 11 11 11 11 0 0
12 12 12 12 12 0 0
13 13 13 13 13 0 0
14 14 14 14 14 0 0
15 15 15 15 15 0 0
16 16 16 16 16 0 0
17 17 17 17 17 0 0
18 18 18 18 18 0 0
19 19 19 19 19 0 0
20 20 20 20 20 0 0
It starts with a list of experiments, sequentially numbered, with a list of pathnames to the relevant xp-files. Note that the xp-files themselves have the reference to the raw data.
Next are the standard global parameters: vbar, hydration (not used yet), solvent compressibility (water is default), and a rotor speed threshold for considering compressibility in the sedimentation models (not implemented yet in version 1.9).
Important are the next entries, the type of model, and the filename where the model parameters are stored. This is a second file with the same name as the 'sedphat' file, but with the extension 'sedphat_PAR'. This sedphat_PAR file contains the settings of the global parameters, and can be loaded separately like a model file (see loading models). However, you don't need to do that when you load a configuration, Sedphat will automatically load the 'sedphat'-file and its associated 'sedphat_PAR' data.
Important: If you move your data to a different computer, you need to copy the sedphat file, the sedphat_PAR file, the xp-files, and the raw data. Further, they need to be in the correct directory structure as indicated in the files. (If you cannot reproduce the directory structure, you can edit the sedphat-file and the xp-files and type the correct directory names.) To save path-independent configurations, see below.
You may notice that Sedphat creates a set of configuration files like the current configuration by preceded by a '~' character during fitting. This is to enable a restoration of the so far best fit.
You can also save a configuration as the startup default, which will cause Sedphat to automatically startup by loading the current data, selecting the model, and having the current parameters. This may be useful, for example, if you have to perform a sequence of similar analyses, or if you want to continue later where you left off.
Slightly different types of configurations can be achieved using the function "Data->Copy All Data And Save As New Config". This function will create a folder with the sedphat extension, along with all the files described above, as well as copies of all the raw data files used.
An example: Let's assume you want to save a configuration termed ABanalysis.sedphat to the folder c:\data. Let's assume the xp-files SV1.xp and SV2.xp are loaded, each of which points to sedimentation velocity experiments with 100 scans (termed 00001.ra1... 00100.ra1 and 00001.ra2...00100.ra2). This function will create a subfolder c:\data\ABanalysis.sedphat, as well as a file of the same name, within that folder. It also creates subdirectories that contain copies of the actual raw data of all the experiments loaded.
The following files can be found:
c:\data\ABanalysis.sedphat\SV1.xp\00001.ra1 ... 00100.ra1
c:\data\ABanalysis.sedphat\SV2.xp\00001.ra2 ... 00100.ra2
The last two lines are folders, each containing copies of the original raw scans. The xp-files SV1.xp and SV2.xp are not pointing anymore to the original raw scans, but to the copies contained in the subfolder. In the xp-files, the third line will read
"_SV2.xp" " 00001.ra2 00002.ra2 ... 00100.ra2"
The underscore "_" preceding the folder name will be the convention that the specified subfolder with the raw data can be found in the same folder as the xp-file itself.
If the complete contents of the folder c:\data\ABanalysis.sedphat (including subfolders with the actual data) is archived or otherwise copied to a different location of the computer, the configuration can find all the necessary files.
It is probably not practical to routinely replace all configurations with path-independent configurations, because this would lead to a proliferation of copies of the original data files on your computer, and require a lot of storage space.