Hi Enrico, Sounds like you are doing everything right. There was a CCP4 alignment problem on some maps (when ncstart, nrstart, nsstart header parameters are far outside map bounds) in Chimera version 1.2444 and earlier. Are you using a newer Chimera version? Another issue is if you have opened several files in Chimera and moved some relative to others, then open the map, the map will be aligned with the model having the lowest opened model id number which may not be the correct model to align with. The Model Panel dialog Transform As... button allows you to correct this. You can look at the volume dialog "Coordinates" panel and see where the origin is set. This is the physical x,y,z coordinates of grid index 0,0,0. If the value is 0,0,0 that indicates that the map header origin values were ignored because they were so large that they looked invalid. (Unfortunately some maps do not initialize them.) You can change it if you can figure out the correct values though that should not be necessary. You can send me the map and PDB if you want me to figure out the exact problem. Tom