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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