[phenixbb] phenix.combine_focused_maps

[Tom Terwilliger]

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 <mks131 at gmail.com> 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: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0010
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