SSDraw

SSDraw is a program that generates publication-quality protein secondary structure diagrams from three-dimensional protein structures. To depict relationships between secondary structure and other protein features, diagrams can be colored by conservation score, B-factor, or custom scoring.

SSDraw also has a colab notebook available at https://colab.research.google.com/github/ethanchen1301/SSDraw/blob/main/SSDraw.ipynb

Installation

SSDraw requires the Biopython and matplotlib modules to be installed.

pip install biopython
pip install matplotlib
pip install numpy

SSDraw also requires DSSP to be installed in order to generate secondary structure annotations:

conda install -c salilab dssp

Alternatively, you can install DSSP either through apt-get (sudo apt-get install dssp), or you can follow the instructions on their github page to make a local installation: https://github.com/cmbi/dssp.

Instructions

SSDraw requires 4 arguments:

1. --fasta: the file name sequence or alignment file in fasta format.
2. --name: the id of the sequence in the fasta file corresponding to your protein of interest.
3. --pdb: the file name of the pdb file of your protein
4. --output: the output file name to use

Example 1:

python3 ../SSDraw.py --fasta 1ndd.fasta --name 1ndd --pdb 1ndd.pdb --output 1ndd_out

Coloring options:

SSDraw uses a gradient to color each position in the alignment by a certain score. The user can choose which scoring system to use, and they can also choose which colormap.

Scoring:

-conservation_score: score each position in the alignment by conservation score.

-bfactor: score each residue in the pdb by B-factor.

-scoring_file: score each residue by a custom scoring file prepared by the user.

-mview: color each residue by the mview coloring system.

Example 2: score by conservation

python3 ../SSDraw.py --fasta aligned.fasta --name 1ndd --pdb 1ndd.pdb --output 1ndd_conservation -conservation_score --start 80 --end 132

Note: for more on how the --start and --end options work, see choosing a subregion.

Example 3: Score by B-factor

python3 ../SSDraw.py --fasta 1ndd.fasta --name 1ndd --pdb 1ndd.pdb --output 1ndd_bfactor -bfactor

Choosing a colormap:

The default colormap for SSDraw is inferno. The user can select one of the matplotlib library color maps or simply list a space delimited set of colors they'd like to use with the --color_map option. Alternatively, the user can select a single color with the --color option and SSDraw will use that color on the whole image.

Example 4: Custom scoring file with custom color map

python3 ../SSDraw.py --fasta 2kdl.fasta --name 2kdl --pdb 2kdl.pdb --output 2kdl_out --scoring_file 2kdl_scoring.txt --color_map black cyan  

DSSP files:

Normally, SSDraw will generate a DSSP annotation from the PDB file, but if you have a DSSP file you would like to use, you can upload it and input the file name in Options.

Choosing a subregion:

If you want SSDraw to draw only a portion of your alignment, you can specify the start and/or end points using the --start and --end options respectively. The argument for these options correspond to the index of the alignment position, not to the residue position numbers. See example 2.

Running on multiple pdbs:

In order to rapidly generate multiple images with SSDraw, we recommend writing shell scripts comprised of commands like those shown in the above examples. For examples of such a shell script, see here.