[phenixbb] Secondary structure weights for realspace refinement

[Oleg Sobolev]

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 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
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20240109/0074d059/attachment.htm>