Quick-Start Instructions


Getting Started with Elves
  1. download Elves.gz
  2. unpack it
  3. Run Elves
That's about it.

Fore more detailed instructions on how to use Elves, please see the Elves Manual.

For an illustrated reenactment of a session with Elves, see the Example Elves Session.


Still Confused? Here's a Short Tutorial:

First, download the Elves script to a unix computer. SGI, linux, Digital unix, doesn't matter, the script should run on all unix platforms.

Run the script with a sentence about what you want Elves to do on the command line. For example, if you are collecting a MAD data set in /data/jamesh/frames from a crystal of a protein whose sequence you have in ~/protein.seq. You would explain this to the Elves like this:

unix% Elves I want you to process the data in /data/jamesh/frames It's a mercury derivative of the protein in ~/protein.seq

The Elves would then examine the files in /data/jamesh/frames, and read the protein sequence from ~/protein.seq. Since you mentioned that it was a mercury derivative, they would check the number of cystines in the sequence and (since you didn't specify otherwise) assume that you have as many mercury sites as you have cystines. A variety of assumptions and deductions like this will be made by the Elves. This takes a few seconds, and then Elves display to you what they think you want them to do, in the form of a short, English paragraph. Then, they ask the question:

Everything look okay? [Yes]
->


Hitting the <Enter> key will give the default response (Yes, in this case). If, however, after reading the paragraph you realize something isn't right, you can either type "no", or simply state what you want changed:

-> actually, there are only 4 mercury sites

Once you type this, Elves will re-display their short paragraph summary again, and repeat the "Everything look okay?" question. You can keep doing this until the Elves get everything right, at which time you would type "Yes" and then the Elves would go write all the scripts needed to implement the procedure they outlined to you, and start running them. Elves try very hard not to bother you from here on out. They will display only the most critical values to your display, and keep all the verbose output from the programs they run on disk, for you to look at if you want.

Once the programs have been run, the Elves will make a suggestion as to what they think the next bext course of action is. For example, if your refined crystal mosaicity changed significantly from the one you initially used, Elves will suggest that you run the refinement again, starting with this new value.

parameters are still drifting, refine again.
Do this now? [Yes]
->


As before, you can hit <Enter> to answer "Yes" or you can describe a different course of action, and the Elves will do their best to follow your advice.

If you redirect Elves output to a file, or use the word "auto" on the command line, Elves will assume you trust their opinion of what to do, and they will simply use the default answers to their own questions, and never ask you anything. This is useful if you want Elves to work on your stuff while you go home for the night. However, in "automatic mode" Elves won't be asking you for confirmation, so make sure you specify everything you want them to do on the command line.

For a comprehensive, verbatim example, see the Example Elves Session.

For a more detailed explanation of how Elves work, please see the Elves Manual.


Back to the Elves Page. 


This page is not finished. It will never be finished, and neither will yours. Admit it.
James Holton <jamesh@ucxray.berkeley.edu>