Protein Artist

This is a repo for simplely fetching and rendering protein 3D structure using Blender Python module bpy.

Table of Contents

• Dependencies
• Usages
• Examples

Dependencies

Dependencies

• python (version 3.10)
• pymol
• bpy

1. Install dependencies by conda:

conda env create -f env.yml

2. Activate conda environment:

source activate blender

Usages

First, set the file access permissions by running

chmod +x renderPDB.py

Then, refer the following usages to run the scripts

usage: ./renderPDB.py [-h] [--id ID] [--camera_lens CAMERA_LENS]
                     [--camera_pos CAMERA_POS] [--core_style CORE_STYLE]
                     [--shell_style SHELL_STYLE]
                     [--temporary_path TEMPORARY_PATH]
                     [--output_path OUTPUT_PATH]
                     [--output_quality OUTPUT_QUALITY]

options:
  -h, --help            show this help message and exit
  --id ID, -i ID        PDB ID or PDB_chain (default: 1IGT)
  --camera_lens CAMERA_LENS, -lens CAMERA_LENS
                        Camera lens. Default 22. (default: 18)
  --camera_pos CAMERA_POS, -pos CAMERA_POS
                        Camera position. Default 140. (default: 40)
  --core_style CORE_STYLE, -cs CORE_STYLE
                        Core structure style. (default: cartoon)
  --shell_style SHELL_STYLE, -ss SHELL_STYLE
                        Shell structure style. (default: surface)
  --temporary_path TEMPORARY_PATH, -tmp TEMPORARY_PATH
                        output file folder name (default: data)
  --output_path OUTPUT_PATH, -o OUTPUT_PATH
                        output file folder name (default: ../img)
  --output_quality OUTPUT_QUALITY, -q OUTPUT_QUALITY
                        output image quality (default: low)

Examples

Render an antibody using default setting

renderPDB -i 1IGT

Render an antibody with different modes

renderPDB -i 1IGT -cs ribbon

Render an antibody with different modes and different views

renderPDB -i 1IGT -pos 40

Render 2019-nCoV RBD/ACE2-B0AT1 complex

./renderPDB -i 6M17