The document discusses protein structure visualization tools essential for analyzing the 3D structures of proteins and biomolecules, highlighting popular software like PyMOL, Rasmol, and UCSF Chimera. Each tool has unique features, installation procedures, and capabilities for molecular visualization, structure manipulation, and analysis. Detailed steps for using each software are provided, emphasizing their importance in drug and vaccine design.

1. PROTEIN STRUCTURE
VISUALIZATION AND COMPARISION
SUBMITTED TO:
Ms.P.MALA
Assistant professor
Department of biotechnology
PMIST
SUBMITTED BY;
MADHUMITHA .S
ll-M.Sc Biotechnology
Computational biology

2. Protein structure visualization
Protein structure visualization tools are software applications that allow users to
view, manipulate, and analyze the three-dimensional (3D) structures of proteins
and other biomolecules.
These tools are essential for understanding the;
• molecular architecture,
• function, and interactions of proteins,
• designing new drugs and vaccines.
There are many protein structure visualization tools available, each with different
features, capabilities, and limitation.

3. Various types of tools are used in protein structure visualization:
It includes;
PyMOL
RasMol
CHIMERA
PyMOL
• PyMOL is a popular and powerful molecular graphics software.
• Editing, and analyzing 3D structures of proteins and other biomolecules.
• PyMOL is written in Python and C, and can be extended and customized with
Python scripts and plugins.

4. Features of PyMOL:
Molecular visualization
Structure manipulation (rotating, zooming, translating)
Selection and labeling of atoms, residues, and chains
Molecular surface and volume calculations
Support for various file formats (PDB, CIF, MOL2, SDF, etc.)
Visualization Options
Cartoon representation
Sticks representation
Spheres representation

5. Steps involved in PyMOL:
Step 1: Installation
• Download PyMOL.
• Install (e.g., Python, OpenGL).
Step 2: Launching PyMOL
• 3D visualization window
Step 3: Loading Molecules
• Open a molecular structure file (e.g., PDB, CIF, MOL2):
• File > OpenDrag-and-drop file into PyMOL window
• Select molecule format (e.g., PDB, CIF):
• File > Open > Format

6. Step 4: Visualization
• Rotate, zoom, and translate molecule:
• Change representation:
• Cartoon
• Sticks
Step 5: Selection and Labeling
• Select atoms, residues, or chains:
• Label selected atoms, residues, or chains
Step 6: Measurements and Calculations
• Measure distances, angles, and torsions:
• Calculate molecular surface area and volume:

7. Step 7: Structure Analysis
• Analyze secondary structure:
• Tools > Secondary Structure
• Detect hydrogen bonds and salt bridges:
• Tools > Hydrogen Bonds/Salt Bridges
Step 8: Scripting and Automation
• Write scripts using PyMOL command language (PyMOL CLI):
• Command line
Step 9: Saving and Exporting
• Save molecular structure:
• File > Save
• Export images and movies:
• File > Export

8. RasMol
• RasMol is a molecular graphics program intended for the visualisation of proteins,
nucleic acids and small molecules.
• The program has been developed at the University of Edinburgh's Biocomputing
Research Unit and the Biomolecular Structure Department at Glaxo Research and
Development, Greenford, UK.
Features of RasMOL
• Molecular visualization
• Structure manipulation (rotating, zooming, translating)
• Selection and labeling of atoms, residues, and chains
• Support for various file formats (PDB, CIF, MOL2, SDF, etc.)

9. File Formats
• PDB (Protein Data Bank)
• CIF (Crystallographic Information File)
• SDF (Structure Data File)
Steps involved in RasMol:
Step 1: Installation
• Follow installation instructions for your operating system (Windows, macOS, or
Linux).
Step 2: Launching RasMol
• Open RasMol on your computer.
• 3D visualization window

10. Step 3: Loading Molecules
• Open a molecular structure file (e.g., PDB, CIF, MOL2)
• Drag-and-drop file into RasMol window
Step 4: Visualization
• Rotate, zoom, and translate molecule
• Change representation(ball,stick,cartoon)
Step 5: Selection and Labeling
• Select atoms, residues, or chains:
• Label selected atoms, residues, or chains:
Step 6: Measurements and Calculations
• Measure distances, angles, and torsions:
• Calculate molecular surface area and volume:

11. Step 7: Structure Analysis
• Analyze secondary structure:
• Tools > Secondary Structure
• Detect hydrogen bonds and salt bridges:
• Tools > Hydrogen Bonds/Salt Bridges
Step8: Scripting and Automation
• Write scripts using RasMol command language:
• Command line
• Use external scripts and plugins:
• Script Editor
Step 9: Saving and Exporting
• Save molecular structure
• Export images and movies

12. UCSF CHIMERA:
Definition:
• UCSF Chimera is a free, open-source molecular visualization and analysis
software tool for displaying, manipulating, and analyzing molecular structures.
• Particularly visualize proteins, nucleic acids, and other biomolecules.
Features:
• Molecular visualization
• Measurements and calculations
• Structure analysis
• Scripting and automation

13. Developed by:
• Resource for Biocomputing, Visualization, and Informatics (RBVI), University of
California, San Francisco (UCSF)
steps to use UCSF Chimera:
Step 1: Installation
Download UCSF Chimera
Step 2: Launching Chimera
- 3D visualization window
- Command line interface (CLI)
Step 3: Loading Molecules
1. Open a molecular structure file
- Drag-and-drop file into Chimera window
2. Select the molecule format (e.g., PDB, CIF)

14. Step 5: Selection and Labeling
Select atoms, residues, or chains:
- Mouse selection
- Command line
Label selected atoms, residues, or chains:
Step 6: Measurements and Calculations
Measure distances, angles, and torsions:
2 Calculate molecular surface area and volume:
Step 7: Structure Analysis
Analyze secondary structure:
Tools > Secondary Structure
Detect hydrogen bonds and salt bridges:
- Tools > Hydrogen Bonds/Salt Bridges
Step 8: Scripting and Automation
- Command line

15. THANK YOU