CS-to-PDB

CS-to-PDB is a standalone Python application that calculates residue conservation from a Multiple Sequence Alignment (MSA) and maps evolutionary information onto three-dimensional protein structures by storing conservation scores in the PDB B-factor field. The resulting structures can be visualized directly in PyMOL and ChimeraX, while an interactive HTML alignment viewer provides a convenient way to compare sequence conservation with structural data.

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Features

• Multiple conservation metrics:
  • BLOSUM62 similarity
  • Shannon Entropy
  • Property Conservation
  • Jensen-Shannon Divergence (JSD)
  • Rate4Site-like weighted conservation
• Optional gap penalty for poorly aligned regions.
• Supports PDB and mmCIF structures.
• Maps conservation scores directly into the B-factor field.
• Generates visualization scripts for PyMOL and ChimeraX.
• Generates an interactive HTML alignment viewer.
• Supports all Matplotlib colormaps, including custom palettes (e.g. MolNympheas).

• Uses identical color palettes for:
  • Protein structures
  • HTML alignment viewer

• PyMOL

• ChimeraX

(small bug with the ramp, I'm working on it)

• Simple graphical user interface.
• Cross-platform (Linux, macOS and Windows).

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Output files

Project/
│
├── protein.pdb
├── conservation.txt
├── visualization.pml
├── visualization.cxc
└── alignment.html

File	Description
.pdb	Protein structure with conservation scores stored in the B-factor field
.txt	Residue-by-residue conservation table
.pml	PyMOL visualization script
.cxc	ChimeraX visualization script
.html	Interactive conservation-colored alignment viewer

Requirements

• Python 3.9+
• Biopython
• NumPy
• Matplotlib
• Tkinter (included with most Python installations)

Install the required packages with:

pip install biopython numpy matplotlib

License

Do whatever you want with the scripts and keep in mind that it has been code by a stupid biochemist (for that matter me).