Hi Manoj, Your command is very close! I think the goal is to combine a total of 7 maps, identifying the relative weights in these 7 maps for 26 regions. This will result in 7 weights for each region, one weight for each map. The sum of weights for each region will be 1. To do this, you want to specify 26 values for "region_selection", one at a time. To get one weight per map, you want to turn off "local_weighting". As you are supplying only full maps, you won't be able to get any half-map output. This yields the following command: phenix.combine_focused_maps \ map_file=Relion_deepEmhancer_reference_.mrc \ map_file=Base_map4.mrc \ map_file=Base_map1.mrc \ map_file=Base_map2.mrc \ map_file=Base_map3.mrc \ map_file=Base_map5.mrc \ map_file=Base_map6.mrc \ model_file=test1.pdb \ region_selection="(chain P and resid 366-401)" \ region_selection="(chain P and resid 179-297) " \ region_selection="(chain O and resid 401-555)"\ region_selection="(chain N and resid 458-530) " \ region_selection="(chain N and resid 311-457) " \ region_selection="(chain R and resid 13-79)" \ region_selection="(chain N and resid 726-577)" \ region_selection="(chain N and resid 823-880)" \ region_selection="(chain I and resid 350-409)" \ region_selection="(chain N and resid 577-726)" \ region_selection="(chain O and resid 667-722)" \ region_selection="(chain Q and resid 264-276)" \ region_selection="(chain N and resid 928-981) " \ region_selection="(chain O and resid 926-971) " \ region_selection="(chain O and resid 875-899) " \ region_selection="(chain Q and resid 208-244) " \ region_selection="(chain O and resid 717-739) " \ region_selection="(chain N and resid 877-898) " \ region_selection="(chain M and resid 7-101) " \ region_selection="(chain L and resid 2047-2141)" \ region_selection=" (chain L and resid 1718-1746)" \ region_selection="(chain L and resid 2001-2025)" \ region_selection="(chain N and resid 880-900)" \ region_selection="(chain P and resid 430-440)" \ region_selection="(chain L and resid 1954-1965)" \ region_selection="(chain P and resid 131-154)" \ composite_map_file=composite_map.mrc \ local_weighting=False \ rigid_body_refinement_single_unit=False \ nproc=8 \ resolution=4.0 Let me know if that does not do it! All the best, Tom T On Tue, May 9, 2023 at 11:30 PM Manoj saxena wrote:

Hi , I am trying the following command using PHENIX VERSION: 1.20.1-4487. to generate a composite map from locally refined maps (cryo-EM) of my complex. I have selected multiple regions each one correspond to one of the six locally refined maps that I wish to combine using this command. I would be grateful if you can suggest if this is the correct way to do it. In this test1.pdb contains the complete model. One of my doubts is that if instead of selection, I supply individual model files for each map region can they have multiple chain Ids. Asking because I was told that I would need to combine all chains and rename them as one chain (per map region) to have the correct weighted map.

Many thanks Manoj

phenix.combine_focused_maps map_file=Relion_deepEmhancer_reference_.mrc map_file=Base_map4.mrc map_file=Base_map1.mrc map_file=Base_map2.mrc map_file=Base_map3.mrc map_file=Base_map5.mrc map_file=Base_map6.mrc model_file=test1.pdb region_selection="(chain P and resid 366-401) or (chain P and resid 179-297) or \ (chain O and resid 401-555) or (chain N and resid 458-530) or (chain N and resid 311-457) or (chain R and resid 13-79) or \ (chain N and resid 726-577) or (chain N and resid 823-880) or (chain I and resid 350-409) or (chain N and resid 577-726) or (chain O and resid 667-722) or \ (chain Q and resid 264-276) or (chain N and resid 928-981) or (chain O and resid 926-971) or \ (chain O and resid 875-899) or (chain Q and resid 208-244) or (chain O and resid 717-739) or (chain N and resid 877-898) or \ (chain M and resid 7-101) or (chain L and resid 2047-2141) or (chain L and resid 1718-1746) or (chain L and resid 2001-2025) or (chain N and resid 880-900) or (chain P and resid 430-440) or (chain L and resid 1954-1965) or (chain P and resid 131-154)" composite_map_file=composite_map.mrc composite_half_map_1_file=composite_half_A_map.mrc composite_half_map_2_file=composite_half_B_map.mrc local_weighting=True rigid_body_refinement_single_unit=False nproc=8 resolution=4.0

-- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: [email protected] Tel: 505-431-0010