Hi Manoj,If you would like to get half-maps produced for combine_focused_maps, then yes, you want to supply half-maps for each focused map.The way it works is that the "full" maps (one for the reference map and one for each focused map) are used to determine the weighting on each map or region with each map.Then these weights are applied to the full maps to create the composite map. The same weights are then applied to the corresponding half maps to create a pair of composite half-maps.Let me know if that does not answer the question!All the best,Tom TOn Mon, May 15, 2023 at 5:00 AM Manoj saxena <mks131@gmail.com> wrote:Hi all,I have a question for generating half half maps for the combined map in Phenix, I am combining 6 regions of a complex (using local refined maps) and supplying the reference map and a reference model for the complex. Additionally, I am supplying the 2 half maps for the whole complex as input fines.I was wondering if I need to supply 2 half maps for each of the local refined regions as input files in addition to the half maps for the reference map.Thank youregardsManoj--Thomas C TerwilligerLaboratory Fellow, Los Alamos National LaboratorySenior Scientist, New Mexico Consortium100 Entrada Dr, Los Alamos, NM 87544Tel: 505-431-0010