Slide 12 of 27
The first step in processing any dataset is to index the images, usually by autoindexing. Mosflm has two autoindexing routines available; the new-style routine uses FFTs, and is used by default as it is very reliable. The indexing can be performed with spots obtained on either a single image or from several.
Fixing the detector distance for this stage is highly recommended. The program prompts for a filename for storing the final orientation matrix (which can be read using the command “MATRIX <filename>”; a maximum likely cell edge is required by the FFT indexing, but the program makes an estimate based on the inter-spot separation, the crystal to detector distance and the wavelength of radiation. Pre-refining before choosing a solution can be helpful in discriminating good high symmetry solutions. The penalties are based on the goodness-of-fit of the 44 lattice characters to the primitive triclinic solution, and are normalised to give a maximum penalty of 999.
Solutions with a penalty less than 200 are presented in a new pop-up window. As a rule of thumb, if nothing is known about the crystal, choose an initial solution in this way;
- note where there is a sharp drop in the penalty - in this case, after solution #10.
- pick the solution with the highest symmetry with a penalty lower than the sharp drop - in this case, solution #10, which is either trigonal or hexagonal. The list of space groups is simply a reminder of the possible choice available;