James Holton

This is me. My name is James Holton. I like to play with molecules. I'm an Associate Adjunct Professor at UCSF, and a Beamline Scientist at 8.3.1 at the Advanced Light Source. For fun, I like to make movies. For my thesis, I created Elves.

Elves are a compact, portable, and intelligent "conversational user interface" to the most common X-ray crystallography programs like CCP4, mosflm, denzo, solve, and shelx. Elves exist as a single text file (shell script) which will run on any unix platform using nothing more than basic unix utilities like csh, awk and grep (plus the executables of the public-domain X-ray programs). Users communicate with the Elves in plain english, and the Elves will then locate, set up and run the appropriate x-ray programs. Elves are not a black box. They work the same way a "human crystallographer" does, by writing, running and editing scripts (.com files).

More recently, I have been developing X-ray diffraction simulators. This is sort of like Elves in reverse: starting with coordinates, and producing a diffraction pattern. Indeed MLFSOM was so named because it is MOSFLM in reverse. This is the most realistic of all my simulators when it comes to the magnitude of the noise, but it is constrained to using a unit-cell formalism for the crystal and fairly simplistic diffuse-scatter model.

For simulating scattering in exotic situations, nearBragg computes the general total scattering from a list of user-specified electrons (slow, but completely assumption-free), and fastBragg computes the diffraction pattern of a small crystal, or even a single molecule given a list of structure factors.

I got my BS in Biology from Caltech. Where I worked in the Mayo group.
I got my PhD in MCB from Tom Alber.

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James Holton <jmholton@lbl>