[phenixbb] [EXTERNAL] Re: Secondary structure weights for realspace refinement

[Reza Khayat]

Hi Oleg,

Thank you for the help. I've defined secondary structures in the header of the PDB and Phenix does recognize these to properly setup the .eff files for refinement. However, am I to increase/decrease sigma, slack, angle_sigma_scale, angle_sigma_set to encourage the dihedrals towards adopting the defined secondary structure? The pop-up bubbles in the GUI do not provide an explanation for these parameters. Alternatively, should I increase the value for distance_cut_n_0 and allow the refinement procedure to do its magic? Thanks again.

Best wishes,
Reza


________________________________
From: Oleg Sobolev <osobolev at lbl.gov>
Sent: 09 January 2024 7:59 PM
To: Reza Khayat <rkhayat at ccny.cuny.edu>
Cc: phenixbb at phenix-online.org <phenixbb at phenix-online.org>
Subject: [EXTERNAL] Re: [phenixbb] Secondary structure weights for realspace refinement

Hi Reza,

There are parameters related to weights of various secondary structure restraints for each element like sigma, slack, angle_sigma_scale, angle_sigma_set for helices and sheets; planarity_sigma, parallelity_sigma, sigma for nucleic acids. The hierarchical list of these is here: https://phenix-online.org/documentation/reference/secondary_structure_restraints.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org_documentation_reference_secondary-5Fstructure-5Frestraints.html&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=6K8j3VgEJ0UG3oRcNSsZAoyWju0j2E73jDKsOYp6efvYNnWQ0FDgW2d6dnlehZaL&s=2XXvWBBG_M9vtaXmTY8VIkA1S5twtYG5r7GMTLtQVuI&e=>
Some of the parameters are available via GUI on "Select atoms" -> "Secondary structure" tab.
For full flexibility one can run the phenix.secondary_structure_restraints command-line tool, edit the resulting parameter file and then supply it to refinement.

Let me know if you have any more questions.

Best regards,
Oleg Sobolev.

On Mon, Jan 8, 2024 at 5:58 PM Reza Khayat <rkhayat at ccny.cuny.edu<mailto:rkhayat at ccny.cuny.edu>> wrote:
Hi,

I hope all is well. Is there a way to alter the weights for secondary structure restraints? 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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