DSSP (Dictionary of Secondary Structure)

DSSP (Dictionary of Secondary Structure) is a tool designed to standardize secondary structure assignment for protein entries.

Key features of version 4.6 include:

• Full mmCIF support: By default, it writes an annotated mmCIF file, storing secondary structure information in the _struct_conf category.
• Poly-Proline helices: This version now defines Poly-Proline helices.

Note: DSSP calculates secondary structure assignments based on existing data; it does not predict secondary structure.

The DSSP algorithm assigns secondary structure based on H-bond energy. The following table maps DSSP codes to their corresponding mmCIF codes and descriptions:

Since version 4.5.2, DSSP includes a Python module that allows you to work with DSSP information directly within Python scripts. To build and install this module, you must enable the BUILD_PYTHON_MODULE flag during the CMake configuration step.

Run the following commands to build and install the module:

git clone https://github.com/PDB-REDO/dssp.git
cd dssp
cmake -S . -B build -DBUILD_PYTHON_MODULE=ON
cmake --build build
sudo cmake --install build

To build the standalone mkdssp program, you need a modern compiler that supports C++20 features. The build process uses CMake and automatically handles downloading and building all necessary requirements.

Follow these steps to clone, build, and install the program:

git clone https://github.com/PDB-REDO/dssp.git
cd dssp
cmake -S . -B build
cmake --build build
cmake --install build

Once the Python module is installed, you can import dssp from the mkdssp package. You can pass the contents of a CIF file (e.g., from a .cif.gz archive) directly to the dssp constructor to extract secondary structure information and residue statistics.

from mkdssp import dssp
import os
import gzip

file_path = os.path.join("..", "test", "1cbs.cif.gz")

with gzip.open(file_path, "rt") as f:
    file_content = f.read()
 
# Initialize dssp with file content
dssp = dssp(file_content)
 
# Access residue statistics
print("residues: ", dssp.statistics.residues)

# Iterate through residues to access properties
for res in dssp:
    print(res.asym_id, res.seq_id, res.compound_id, res.type)

A complete list of available command-line options for mkdssp.

--output-format=[dssp|mmcif]
--no-dssp-categories
--min-pp-stretch
--write-other
--components
--extra-compounds
--mmcif-dictionary

Advanced configuration for helix assignment and compound knowledge:

• --min-pp-stretch: Defines the minimal number of residues with PHI/PSI angles within the required range to assign a PPII (Polyproline II) helix.
• --components: Specifies a custom CCD file to load compound knowledge. This overrides the default components.cif installed by libcifpp.
• --extra-compounds: Allows adding additional files (in CCD format or CCP4 restraints format) to the standard components.cif file.
• --mmcif-dictionary: Specifies a custom mmCIF dictionary file, overriding the default installed by libcifpp.

Use the following options to control the format and content of the generated secondary structure files:

• --output-format=[dssp|mmcif]: Forces the output format. Use dssp for the old fixed-column format or mmcif for the new annotated mmCIF format.
• --no-dssp-categories: When writing mmCIF files, this suppresses the output of all dssp_ categories.
• --write-other: By default, the mmCIF format does not write structure information for the OTHER category. Use this flag to include it.

mkdssp --output-format=dssp input.pdb output.dssp

mkdssp --output-format=mmcif --write-other input.cif output.cif