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@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@lbl.gov>
Sent: 09 January 2024 7:59 PM
To: Reza Khayat <rkhayat@ccny.cuny.edu>
Cc: phenixbb@phenix-online.org <phenixbb@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

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@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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