Hi Hernando, A map in Chimera has a coordinate system where the x,y,z position of the data value at grid index 0,0,0 can be anywhere, and the spacing between grid planes along the 3 grid axes can be any distance. Those parameters for a given volume are shown in the Coordinates panel of the Chimera volume dialog (1.2470 and newer). The values come from the map file header. They can be changed and you can save a new map if desired. In general an atom placed at x,y,z = (0,0,0) will not be at the middle of a map. A PDB file has an xyz coordinate system and the atom coordinates are given in the PDB file. If you open a map and a PDB model then their xyz coordinate systems are the same. But if you freeze the map (for example, with the "active" button on the model panel) and move the PDB model, then the coordinate systems of the PDB and map no longer match up. There is a rotation and translation relating the two coordinate systems that Chimera remembers. This is where saving the PDB relative to the map is handy. The PDB atom positions get written out using the coordinate system of the map with that setting, instead of relative to the molecule's coordinate system. I don't know how you are rotating the the molecule. Most methods (e.g. movement with mouse) use a center of rotation that is not xyz = (0,0,0) since that may be far off the screen. Usually Chimera uses the center of the bounding box of the displayed molecules and maps as a rotation center. Another choice is to have the rotation center fixed in the middle of the screen and midway between clip planes in depth. Or it can be fixed at specific coordinates. The current setting is shown using menu entry Tools / Movement / Rotation. Hope this clarifies some of the coordinate system workings. Tom