Xfit and Probe
What is probe?
Probe is a program written by J. Michael Word in Dave and Jane Richardson's lab that calculates the intersection of tiny probe surfaces. This shows the contacts between atoms (A below). As the contacts get closer and the overlap greater, probe colors the surfaces more dramatically (B below).
In the new xfit, probe is interactive - as the model is changed, probe is called and the surface updated. This happens fast enough to be used in real time.
How do I use probe with xfit?
First get the new xfit v4. Then get probe and install it in your path. You will also need a new colors.dat file. Put this file either in the current working directory or in $XTALVIEWHOME/data. Then start the new xfit, load a model and set up a residue to be fit (click a residue and select Fit: Residue on the main window). To turn on the surface right click on the button under Surface: on the main window and choose Tiny Probe). Try changing the residue by moving the mouse into the canvas (click to get focus on some machines) and press the 1 key to activate the chi1 torsion. Drag with the middle mouse to change chi1. As you do so the surface should change.
If it doesn't work make sure you have xfit v4. Make
sure probe is in your path and runs. Type probe at the command prompt.
You should get a help screen for probe. If the colors look funny
make sure the new colors.dat is either in the directory you start xfit
in or in the $XTALVIEWHOME/data directory.