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How to Convert Ultracentrifuge Raw Data to UltraScan III AUC Format

With us_convert, you can import and convert experimental raw data, acquired using an ultracentrifuge, into a set of files written in the UltraScan III OpenAUC format. An AUC file is a binary file that contains all the information from a single dataset (cell/channel/wavelength combination, also called a triple) imported and converted from the original raw data format. So if the raw experimental run contained data in three channels us_convert would convert that into three binary AUC files, which can then be uploaded to an UltraScan III database and prepared for analysis. The AUC file format is described here.

US_Convert Window

Using this window, you can convert raw data located on your local disk, and then store the resulting AUC file(s) on your local disk or in the current database. You can save the information on local disk and then synchronize your data with the database later if you prefer. You must be identified as the investigator (or data owner) to delete or update a converted AUC file in the database.

The first step is to select either the Database or the Local Disk radio button at the top of the window. This indicates your primary data repository at the moment. Many buttons are affected by this--- loading and saving data, including support information like buffers and projects, will look at these radio buttons to determine where to perform their tasks. You may switch back and forth as you work, for instance loading solutions from database and then saving them to disk so that they will be available later when you are not connected to the Internet.

STEP 1: Loading Data

To load data into the application, do one of the following:

STEP 2: Editing the run information

Click on the "Edit Run Information" button to open a Managing Experiment Information dialog.

You can view some of the details by clicking on the "Run Details" button.

STEP 3: Verifying the RunID

The runID must be a unique string of characters. Normally it is the directory name from which the raw data was loaded and converted, but if you re-import the data you will encounter a naming conflict in the database, because another run by the same name already exists in the database. To avoid this, go to the edit box labeled "Run ID:" and change the name to a name that is unique in the database. You should make this this name change first, since this edit box will be disabled in the next step.

STEP 4: Cell/Channel/Wavelength Triples

The different cell/channel/wavelength (c/c/w) combinations will appear in the listbox to the left. You may click on each of these to see the data from that c/c/w. First, select the centerpiece that was used from the drop-down list. Then create or select a solution for each c/c/w in the data. Click on the button labeled "Manage Solution" to associate a solution for the currently selected c/c/w, by opening a Manage Solution Information dialog. You may wish to use the "Apply to All" button to copy solution information from the currently-selected c/c/w to all the others. You could then select exceptions and associate a different solution for that c/c/w if you wish. Click on the "Show Intensity Profile" button to see the intensity profile if you wish.

Note that for Multi-wavelength (MWL) data, the contents of the left-side listbox is actually cell/channel entries, with wavelengths represented as a range of wavelengths and with a count of wavelengths shown in parentheses. The MWL special elements are detailed below.

STEP 5: Handling Special Cases

Depending on the type of data being converted, additional processing may be required. In the following paragraphs we describe how to process these types of data, followed by a snapshot.

Radial Intensity Data (Beckman suffix "RI"). First, select the c/c/w that you wish to be defined as the reference. Then click on the button labeled "Define Reference Scans" and control-click the range you wish to use in the plot. That is, hold the control button down on the keyboard while clicking the left mouse button. Control-click on two points in the radial range that corresponds to a clean, noise free region in which the reference data can be found. This is typically the air region above the meniscus, but it can also be a channel that contains air or water. The program will use the reference data to convert the radial intensity data to pseudo absorbance data. Next, you can click on "Drop Current c/c/w" for each of the reference channels you don’t need any more, or you can click on "Undo Reference Scans" to undo the reference scan processing and do it again.

Converting RI data to pseudo-absorbance data

Multiple channels. In cases where you used a 6 or 8 channel centerpiece, you will have multiple channels in a single channel, which need to be separated into individual c/c/w triples. You can define subset c/c/w combinations by clicking on the button labeled "Define Subsets" and then control-click at the radius that separates columns. Do not click at the the starting and ending radius for the entire dataset---these are assumed. When you are finished, click on the "Process Subsets" button and the c/c/w combinations will be separated out. You will need to do this for each of the original datasets in the data.

    Subsets in RA Data

Wavelength Data. In wavelength data the datasets are separated by radius instead of wavelength, and so we have c/c/r combinations. In order to separate the datasets into wavelength data, the tolerance level between datasets has to be adjusted to a smaller number. Us_convert chooses 0.1 cm as the separation tolerance for wavelength data, however you might decide that you would like to use a different number. If so, you can adjust the tolerance in the "Dataset Separation Tolerance" box, above. As you change it the c/c/r combinations will adjust dynamically.

Adjusting Tolerance Between Datasets

MWL Data. In multi-wavelength data, there are many triples. But selection is generally done by chosing a cell/channel and then adjusting the range of wavelengths within that channel. Some of the additional GUI elements and their corresponding options for MWL include the following.