Hi Puey, Chimera just allows hand placement and local computational position optimization of atomic models in EM maps. It does not do any global search for the best location in the map. The hand placement is done by freezing the map so it is not moved by the mouse. Do this using the Model Panel dialog (menu Favorites / Model Panel) and click off the switch in the second column (with heading "Active") to lock the map position. Then move the atomic model with the mouse. It usually requires locking and unlocking the map many times to view the hand positioning from different angles. Mesh display or transparent surface display for the density map is useful. Once you get the position approximately right you can do a computational position optimization that rotates and translates the atomic model so that the sum of the density values at the atom positions (interpolated map values) is maximized. To use this select all atomic model atoms (ctrl-left-mouse click one atom and press the up arrow key a couple times, or use menu Select / Select All (assuming just one atomic model is open). Then use menu entry "Tools / Volume Data / Fit Models in Maps" and press the Fit button. It typically takes about 10 seconds then moves the atomic model to the locally optimal position. You can undo the motion using menu entry Tools / Movement / Undo Move. The goodness of fit is reported as the average density value at the positions of the selected atoms. Those values appear in the Fit dialog status line and also the Reply Log (menu Favorites / Reply Log). Tom