Chapter 1: Starting the Program and Setting the Data Sets

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Step 5: Setting up Data Files

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Step 5: Setting up Data Files

Select the frames to be processed using the load data sets button (Figure 7) and single clicking on one or more sets of frames.  

Figure 7. The Load/Create New Sets window 

*  Avoid assigning frames with the names ending in string of 5 or more numbers because the set parser cannot distinguish a contiguous data set among the frames. For example, if the root of your data file names is nc401, and then you collected frames 001 through 140, you expect files called nc401001.img through nc401140.img. Unfortunately, it is very difficult for a computer to parse this type of file name and distinguish between: 1-140, 1001-1140, or 401,001-401,140 frames. You may keep a root nc401, but add other characters, for example: nc401_set1_0001.img, nc401_set 2_0001.img ...

 

What am I looking at in the dialog box that pops up?

 

If you have not clicked on one of the little boxes below the load data sets button, you should just see what the program considers to be the sets of data frames with # signs standing for wild card frame numbers (Figure 8). Click once on the set of frames you want to process - it will turn blue - then hit OK.

 

Figure 8. The Load Data Sets window

 

After pushing the edit set(s) button (Figure 12)  you should see the Raw Data Dir, Output Data Dir and File Template boxes filled in, along with the starting number and the number of frames (Figure 9). If you are processing data concurrently with the data collection and data collection is not performed by HKL-2000 you can edit manually Number of Frames box and integration will wait for incoming frames.

 

Figure 9. The Edit Set(s) window

Should I click Show All Sets?

Usually it is not necessary because the normal file selection procedure works fine if the site is set up correctly and the proper data suffix has been specified. However, this option is still useful because you can navigate through the directory tree after activating the show all sets button (Figure 7).

How to recover from ambiguous name schemes?

Change the name in File Template from nc######.img into nc401###.img and move mouse. Program will check the frames and dialog box will ask for approval. After OK hit, the proper values of First Frame Number and Number of Frames should appear and File Template will be automatically adjusted according to new scheme.

What if I don't see any frames listed?

This means that either you have no data frames in the New Raw Data Directory, or else they are not named and numbered in a way that the program can identify them as data frames. For example, your files may be of the form *.mccd, but the Site Information file is expecting files with the suffix *.img. The best way is to go to Site Configuration and edit Predefined File Template. Alternatively, you can try clicking on the show all sets button before clicking on load data sets, and this will open a new window: Select Data Sets - Show All Files with all of the files in the New Raw Data Directory (Figure 10). In the window you can manually define a file template as well as a set start and end.

 

Figure 10. All files are listed after activating the Show All Sets button

Why would I want to click Scale Sets Only?

This will display only the .x files that in the New Raw Data or New Output Data directory paths (Figure 11). You might want to do this if you were just interested in scaling the integrated data, rather than re-indexing and re-integrating the raw frames, and the raw frames were no longer on your disk drive.

 

Figure 11. Files listed after activating the Scale Sets Only button

Can I click more than one set of data? Why would I want to do this?

Yes, you can click on several sets of data within the select data window. Clicking once selects, clicking again deselects. You do not have to hold down any additional keys to select more than one just click on what you want.

As to why you might want to do this; this is extremely useful when you have collected multiple data sets from a single crystal and want to process them all together. Examples of this include:

1.  inverse-beam experiment,

2.  data sets which differ by the 2q offset of the detector,

3.  low-pass and high-pass data sets that differ in the crystal-to-detector distance,

4.  multi-wavelength experiment.

In all cases, if the goniostat is aligned (and this alignment must be in the site file) and if the crystal has not been moved relative to the goniostat, and if the header information of the image files is reasonably accurate (so that detector distance and position information is present), then you should be able to process all of the frames together from a single autoindexing.


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