[phenixbb] Phenix resolve_cryo_em with local resolution

[Tom Terwilliger]

Hi Reza,

I just tested the use of the keyword:
   adjust_local_resolution_coloring=True
in resolve_cryo_em and it seems to work fine for me.  This keyword only
affects the local resolution map (not the density-modified map).

Perhaps you might want to update your Phenix version to get this command
to work.  Here the current release version:
   https://phenix-online.org/download/phenix/release/

If your goal is to get a map that is adjusted based on local resolution,
you may want to use instead the keyword:
    sharpening_type=local_final_half_map
which applies local sharpening in the final cycle of density modification.

All the best,
Tom T

On Sun, Apr 28, 2024 at 9:30 AM Reza Khayat <rkhayat at ccny.cuny.edu> wrote:

> Hi,
>
> Is it possible to run resolve_cryo_em and have it consider the local
> resolution of the two half maps in the final map? I have a 3.7Angstrom map
> were certain domains, too small for local refinement with single particle
> analysis, are smeared out in the resolve_cryo_em map. Their densities are
> stronger when I low pass filter the original maps. The
> adjust_local_resolution_coloring = True option seems to be what I need;
> however, including this option in the command line results in:
>
> Please run this program with the --show-defaults option to see what
> parameters
> are available.
>  PHIL parameters in files should be fully specified (e.g.
> "output.overwrite"
> instead of just "overwrite")
>
> The command line I use is:
> phenix.resolve_cryo_em map_file_name=Class001_full_box_40.ccp4
> half_map_file_name_1=Class001_half1_box_40.ccp4
> half_map_file_name_2=Class001_half2_box_40.ccp4 resolution=4.0
> dm_resolution=3.5 cycles=1 box_before_analysis=False
> density_modify_unsharpened_maps=True nproc=16 force_nproc=True
> model_1=Class001.pdb seq_file=Class001.fasta ncs_copies=1
> output_directory="Class001_local" adjust_local_resolution_coloring=True >
> Class001_local.log
>
> Any help would be appreciated. Thanks.
>
> Best wishes,
> Reza
>
> Reza Khayat, PhD
> City College of New York
> Associate Professor
> Department of Chemistry and Biochemistry
> Co-Director NIH G-RISE program
>
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-- 
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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