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

[Oleg Sobolev]

Hi Reza,

The parameters I mentioned previously control the weight (strength) of the
SS restraints that are established.

To avoid rejection of your (presumably hand-curated) secondary structure
annotations from PDB header, you can set
secondary_structure.protein.remove_outliers=False
Setting distance_cut_n_0 to a large number would have similar effect. Both
of them can be changed if you search for them in GUI "All
parameters"->"Search parameters". I would start with the remove_outliers
parameter.

Best regards,
Oleg Sobolev.

On Wed, Jan 10, 2024 at 4:14 AM Reza Khayat <rkhayat at ccny.cuny.edu> wrote:

> 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> 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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