Hi Hernando, The details about how fitting models in maps is works are described in the Chimera manual. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmodels/fitmodels... You can display the manual page by pressing the Help button on the Fit Models in Maps dialog. Briefly, it does not compute a density from the atomic model -- that would require you specify a resolution if you wanted a meaningful cross correlation value. It simply looks at interpolated density values at the atom positions and maximizes their sum. It uses gradient descent and typically translates by no more than about the molecule radius and rotates by no more than about 90 degrees. There are no coded limits though. For step sizes and convergence criteria see the manual. A few weeks ago I wrote some code to fit a map in another map and report the correlation coefficient: http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-November/001105.html This will be part of Chimera in the next snapshot releases. It still does not compute a density from a PDB model so you would have to do that with an external program. We will add that capability in the future. Tom