Hi Tom,
Thanks for the help. I'll update Phenix and try both keywords independently.
Best wishes,
Reza
________________________________
From: Tom Terwilliger
Sent: 29 April 2024 7:37 AM
To: Reza Khayat
Cc: [email protected] ; Tom Terwilliger
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/https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org_download_phenix_release_&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=mf-ehEYABci8Qhn6z96_zEzcDai2rWaKOlYkSIkWlAreVPTr_rUlEWF2tVtZR1u1&s=WpWruLHR8cbbvydH2FwoFAkighnCk-oAZ0uBMuyXr5U&e=
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 mailto:[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
Email: [email protected]mailto:[email protected]
Tel: 505-431-0010
