phenix.secondary_structure_restraints

Description

It is a tool to generate secondary structure annotation in various formats using pdb file. When HELIX/SHEET records are present in input pdb file, no searching occurs, they are used as source of information about protein secondary structure. To force automatic detection of protein secondary structure elements, one needs to remove them from input file.

There are several methods available to search protein secondary structure:

Output format:

Command line usage examples

% phenix.secondary_structure_restraints model.pdb

% phenix.secondary_structure_restraints model.pdb format=phenix.refine

% phenix.secondary_structure_restraints model.pdb ignore_annotation_in_file=True

% phenix.secondary_structure_restraints model.pdb search_method=from_ca format=pdb

GUI

Graphical user interface is currently available under phenix.refine GUI, "Refinement settings" tab, select "Use secondary structure restraints" checkbox and click "Select Atoms" button.

List of all available keywords