Q: How can I figure out the correct parameters for the xfiles argument? I know that the first argument is the angstrom per pixel (which is, say, 2.1), and I know that my molecule weighs a certain amount (say, 1700 kDa). I am not sure of the third argument, but I am aware that it might be practically unused. Is it as simple as writing xfiles=2.1,1700,99?

A: This is actually documented in the refine documentation I believe, but essentially the above is correct. The 3rd parameter allows you to align models rotationally to the results from a particular iteration. Since there typically aren't 99 iterations, this number effectively disables this option. Frankly the main point is for asymmetric structures to prevent them from 'drifting' rotationally from iteration to iteration, but is rarely used. Also note that the volume adjustment based on specifying the mass is only approximate, and only vaguely useful in absolute map evaluation. It is, however, useful to make sure that the same isosurface threshold can be used from one iteration to the next.

EMAN1/FAQ/XFiles (last edited 2008-11-26 04:42:29 by localhost)