At the bottom of RnallViewer's main window are three fields. The left two are for some textual feedback -- the top has a simple hyperlink navigation system to go through screens showing the results of running some background executables -- for example, the CT file shown in the picture. The bottom left field shows some more low-level interaction -- the actual system calls used and any messages received back.
To the right is where the result of a call to ghostscript will go -- an image pops up corresponding to the CT file.
Finally, at the bottom are some analysis tools. You can set or append structures using the output file from Rnall, which in turn has input based on a variable region chosen from the second pop-up. Alternatively you can use an external file. You can manually set the window sizes and energy cut-off level (if the structure's energy is above the cutoff, no CT file and thus no image file is generated). Below this lets you interact more directly with the conversion process from CT file to image file.
When you run Rnall for just one specific structure, it generates a CT file, which is sent along to naview, then plt22ps, then ghostscript, and finally loaded as a jpeg on the right. In the textual output field at the top, you can view and save the different parts of this process. If you encounter any troubles, double-check the system field below.