Hi Tom,

Thanks for the help. I'll update Phenix and try both keywords independently. 

Best wishes,
Reza
From: Tom Terwilliger <[email protected]>
Sent: 29 April 2024 7:37 AM
To: Reza Khayat <[email protected]>
Cc: [email protected] <[email protected]>; Tom Terwilliger <[email protected]>
Subject: [EXTERNAL] Re: [phenixbb] Phenix resolve_cryo_em with local resolution
 
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 <[email protected]> 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
Tel: 505-431-0010