Chapter 1: Starting the Program and Setting the Data Sets

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Step 4: Output data files

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Step 4: Output data files

 

Set up your output files using the Directory Tree and Output Data Dir. The suggested convention is to have a subdirectory called proc in the directory that holds your frames, for the files created during data processing.

 

I don't see the ../proc directory. How do I make one?

To make a proc subdirectory, single click on the folder under which you want to create this new directory (Figure 4). Usually this will be within the directory that contains your frames. For example, if your frames are in /data/gewirth/X25/complex, then the proc would be a subdirectory within complex, i.e. /data/gewirth/X25/complex/proc. Click on create directory and a dialog box will open with the path displayed. Append your subdirectory name onto the end of this path. When the set is already created you can change data output directory by right mouse button click only (Figure 6).

Figure 6. The Output Data directory

Do I have to have a ../proc directory, or can I put the files anywhere?

 

You can put them in your parent directory, or you can put them in the same directory as the frames. The nice thing about having proc subdirectories is that if you reprocess the data you can have a different proc (e.g. proc1, proc2, proc_p222, proc_p21, etc.) subdirectory for each attempt and not worry about overwriting data or having to think of new file names all the time.

 

How much disk space am I going to need for this?

Each indexed raw data file yields a new file, called an .x file, with the extracted spot information from the frame in it. The .x file size is therefore a linear function of the number of reflections on the image. As you might imagine, the .x files for a lysozyme data set would be quite a bit smaller than those for a ribosomal subunit data set when the crystal diffracts well. Generally, the .x file size depends on the unit cell and resolution. You always should have at least 10% of your disk space free.


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