Hi Alexander, The "fit models/maps in maps" tools in Chimera just do a local position and orientation optimization. So the first requirement is that you put the model in approximately the correct place. The fit models tool is trying to maximize the average density at the selected atom positions. The fit map in map tool maximizes the sum of the products of the two maps at positions within the shown contour level. If the map you are fitting into has a region with higher density than all the surrounding regions then no matter where you start the model it may be pushed into that high density part of the map. This happens if there are no intervening low density regions between the initial placement of the model and high density area. If this is the situation then these tools may simply not be useful for you. This is a common situation. Perhaps no boundaries between the 3 fragment models you are trying to fit is apparent in the density map. A more sophisticated kind of fitting would be needed than what Chimera provides. A capability we would like to add to Chimera but is not available now is to place 2 of your 3 fragments by hand and then fit the 3rd fragment in the map while avoiding steric clashes with the others. Another capability that could be of use to you but is not in Chimera is fitting a map in another map using correlation. Instead of maximizing the sum of products of density, a normalization is done so only the match between variations in density (high density matches high, low matches low) is optimized, and the fit is not pushed towards higher density regions that do not have good matching variations in density. Other programs that do global fitting usually optimize correlation. Here are two ways you can use Chimera that could help. If you can combine your 3 fragments into a single PDB model with a variety of conformations (maybe you consider 5 plausible arrangements of domains). Then that 3-domain assembly can be fit into the map with "fit models in maps" and the scores for the hypothetical conformations can be compared. Another possibly useful tool is volume eraser. If the asymmetric units in your map are not separated by low density you could use volume eraser (Tools / Volume Data / Volume Eraser) to erase all but one asymmetric unit. That may simplify fitting. You could go further and erase parts of the density for one PKC to force the fit of a fragment to stay in the unerased part of the density. It sounds like you have tried restricting display of the density to a subregion (Volume Viewer dialog subregion selection). That has a similar effect but only allows you to use rectangular subregions, where the eraser tool lets you erase any part of the map. You may see that the fit model gets pushed partly outside the bounds of the map. That is because the atoms outside the map do not contribute to the optimized "average density at atom positions". So if the highest density of the map is right on the edge of the box then the model will get pushed partly outside to get best overlap with that high density. Another technique for erasing part of the density is to place some models in the map, use the color zone tool to color the map within a certain range, then use the "split volume by color zone" plugin (available from http://www.cgl.ucsf.edu/chimera/experimental/experimental.html) to get just the density near that placement of the model. Then try the fitting tools within that more limited density. Tom