[phenixbb] [EXTERNAL] Re: Phenix resolve_cryo_em with local resolution

[Reza Khayat]

Hi Tom,

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

Best wishes,
Reza
________________________________
From: Tom Terwilliger <tterwilliger at newmexicoconsortium.org>
Sent: 29 April 2024 7:37 AM
To: Reza Khayat <rkhayat at ccny.cuny.edu>
Cc: phenixbb at phenix-online.org <phenixbb at phenix-online.org>; Tom Terwilliger <tterwilliger at newmexicoconsortium.org>
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 <rkhayat at ccny.cuny.edu<mailto: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

_______________________________________________
phenixbb mailing list
phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
http://phenix-online.org/mailman/listinfo/phenixbb<https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_phenixbb&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=mf-ehEYABci8Qhn6z96_zEzcDai2rWaKOlYkSIkWlAreVPTr_rUlEWF2tVtZR1u1&s=OWfKVwQA6Th-U60PNOXs85foW1vTiAQ1PhRrG_YDK4k&e=>
Unsubscribe: phenixbb-leave at phenix-online.org<mailto:phenixbb-leave at phenix-online.org>


--
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<mailto:tterwilliger at newmexicoconsortium.org>
Tel: 505-431-0010

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20240429/1d71fb6a/attachment-0001.htm>