[phenixbb] [EXTERNAL] Re: Question about phenix.resolve_cryo_em

[Reza Khayat]

Hi Tom,

Thanks.

Best wishes,
Reza
________________________________
From: Tom Terwilliger <tterwilliger at newmexicoconsortium.org>
Sent: 18 November 2023 11:44 AM
To: Reza Khayat <rkhayat at ccny.cuny.edu>
Cc: phenixbb at phenix-online.org <phenixbb at phenix-online.org>
Subject: [EXTERNAL] Re: [phenixbb] Question about phenix.resolve_cryo_em

Hi Reza,

If you use a model in density modification with resolve_cryo_em, it is necessary to create a multi-model ensemble with refinement in order to reduce model bias. For details on why this works and is necessary, see:

https://scripts.iucr.org/cgi-bin/paper?S205979832001061X<https://urldefense.proofpoint.com/v2/url?u=https-3A__scripts.iucr.org_cgi-2Dbin_paper-3FS205979832001061X&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=JqRoNWgCMUo6tg22Jsy7a8OEgOA1DYAEEue1Jb9bwl0cSZCqeImqLA2xZk3c2xn_&s=j9eKWCQRvD9s6WmS7eS7IlKc5SMw1p3aa4YUJ_pbXzU&e=>

All the best,
Tom T

On Fri, Nov 17, 2023 at 4:00 PM Reza Khayat <rkhayat at ccny.cuny.edu<mailto:rkhayat at ccny.cuny.edu>> wrote:
​Hi,

Is it possible to turn off the model refinement procedure in phenix.resolve.cryo_em and go straight into density modification? My current model fits reasonably well. Also, Does the routine work well with nucleic acid (e.g. something like RNA from ribosome)?

Best wishes,
Reza
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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<mailto:tterwilliger at newmexicoconsortium.org>
Tel: 505-431-0010

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