"Because You Have Better Things To Do"TM




Elves are the first "expert system" for the processing of x-ray data from macromolecular crystals. They work by overlaying the script-driven interfaces of common x-ray programs with simple, free-form unix commands like this:

unix% Elves I want you to process the data in /data/jamesh/frames using the protein sequence in ~/orf.seq

Elves will know what to do if you type the above command line. No, really, they will! In fact, this is about all the information they need about your project. An example of how Elves respond to this command is available here.

Elves automate most of the repetitive and mindless procedures used in solving macromolecular crystal structures, and they are capable of autonomously carrying out all the steps needed to convert raw x-ray diffraction image data to a phased electron density map. Although user input is not necessary for Elves to acomplish this task, the real power of Elves is that it is easy for crystallographers to communicate with them in English. Thus, providing the most intuitive interface possible between the crystallographer and his/her x-ray data.

Elves also work "out of the box." The Elves program is self-configuring, so you don't have to set up Elves on your compter system. Since Elves exist as a single text file, (a shell script) they can simply be copied or emailed to any new unix system, and then they are ready to run. You don't have to write an "Elves script", and you don't have to convert any file formats. Elves simply use the file formats of the programs they run.

There are also no new programs to learn. Elves use standard x-ray data processing programs: mosflm, ccp4(required), shelx, SOLVE, and, (if possible) wARP. Like a "real" crystallographer, Elves use these programs by writing and editing scripts. However, unlike a real crystallographer, Elves do this very, very fast. Starting with only the images from a newly-collected MAD data set, they can produce an electron density map in a matter of hours on a reasonably fast computer. When they are finished, Elves will leave you with all the scripts, logs, and processed data they used to get you as far as they did, just like a colleague handing over a project. This way, even if Elves fail, you can still continue working from where they left off.

Wether you are an advanced user, or are just beginning to solve your first structure, Elves are a great time-saver for getting things started with each new crystal, and for learning how to use the standard x-ray programs. After all, don't you have better things to do?


Get Elves

Quick-start Instructions

Elven Goodies

Frequently Asked Questions (with Answers)

Example Elves Sessions

The Elves Manual

Known Bugs

Citing Elves


Back to the Alber Lab.


This page is not finished. It will never be finished, and neither will yours. Admit it.

James Holton <jamesh@ucxray.berkeley.edu>