[phenixbb] phenix.combine_focused_maps

[Manoj saxena]

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
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