Workshop - PyMol or ChimeraX

Kumar Nagarathinam

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Workshop - PyMol or ChimeraX
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FREE
30 mins

PyMOL Workshop


Getting Started with PyMOL

  1. Introduction to PyMOL and Its Applications
  2. Installing and Setting Up PyMOL
  3. Exploring the Interface and Basic Navigation
  4. Loading and Viewing Molecular Structures
  5. Representations: Cartoon, Sticks, and Surface


Visualization and Customization

  1. Advanced Representations and Coloring
  2. Highlighting Specific Chains, Residues, and Ligands
  3. Selections: Commands and Named Selections
  4. Measuring Distances, Angles, and Dihedrals
  5. Annotating Structures with Labels and Text


Molecular Analysis

  1. Protein-Ligand Interactions: Binding Sites and Key Contacts
  2. Surface and Volume Visualization
  3. Hydrogen Bonds, Salt Bridges, and Pi-Stacking Interactions
  4. Aligning and Superimposing Structures
  5. Exploring Molecular Dynamics Snapshots


Scripting and Automation

  1. Introduction to PyMOL Command Language (PML)
  2. Writing and Running Basic Scripts
  3. Automating Repetitive Tasks with Loops
  4. Batch Processing of Multiple Structures
  5. Hands-on Exercise: Custom Scripts for Data Analysis


Advanced Techniques and Applications

  1. Creating Publication-Quality Images
  2. Animations and Movies for Molecular Presentations
  3. Exploring Real-World Case Studies
  4. Tips and Tricks for Effective Molecular Visualization
  5. Q&A, Wrap-Up, and Certification (if applicable)


ChimeraX Workshop


Introduction to ChimeraX and Basic Visualization

  1. Overview of ChimeraX and Its Uses
  2. Installing and Setting Up ChimeraX
  3. Navigating the ChimeraX Interface
  4. Loading and Viewing Molecular Structures
  5. Basic Visualizations: Sticks, Ribbons, and Surfaces
  6. Basic Commands and Mouse Control


Advanced Visualization and Analysis

  1. Customizing Visual Styles and Colors
  2. Measuring Distances, Angles, and Dihedrals
  3. Protein-Ligand Interactions: Visualizing and Analyzing
  4. Surface Visualization and Electrostatic Potential Maps
  5. Structural Alignment and Superimposition
  6. Visualizing Molecular Dynamics Trajectories


Scripting, Movie Creation, and Applications

  1. Introduction to ChimeraX Command Language
  2. Writing and Running Simple Scripts
  3. Creating High-Quality Publication Images
  4. Generating Molecular Animations and Movies
  5. Real-World Case Studies and Applications
  6. Q&A, Recap, and Wrap-Up


This workshop will provide a solid foundation in ChimeraX, including essential visualization, molecular analysis, and practical applications.


This workshop offers a comprehensive approach to mastering PyMOL and ChimeraX, guiding participants through everything from basic navigation to advanced visualization, analysis, and scripting. By the end of the workshop, attendees will be equipped with the knowledge and skills necessary to effectively utilize both software packages for molecular research and presentations.


Will charge a fair price based on the number of students and days.

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