Okay, a fairly mundane question concerning random seeds in Phenix. Obviously they are random but any restrictions on how many digits phenix will accept?
It is determined by the random number generators we're using. Up to 9 digits should be fine. I'm not quite sure what the exact limit is.
Any other restrictions?
Don't think so. Any integer up to a certain limit should work.
Are they (it) only used for coordinate refinement
Any time the weight calculation is involved random numbers enter through the assignment of random velocities for a short Cartesian dynamics calculation. This is used to "shake" the model before computing x-ray/neutron gradients and restraint gradients. The weight is determined as the ratio of the norms of these gradients (after outlier removal).
or do the random seeds get used for other things as well?
The weight calculation and Cartesian or torsion-angle simulated annealing are the main uses. Beyond that it takes a closer look to know if random numbers enter into a particular procedure. Ralf