Cookbook

Welcome to the MolSysMT Cookbook. Here, you won’t find dry API descriptions; instead, you will find ready-to-use recipes to solve complex structural biology tasks with elegance and speed.

Each recipe is designed to be a “Superpower”: a self-contained solution to a real-world scientific problem.

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🏛️ Engineering & Construction

• Building Complex Dimers: Harvesting, aligning, and merging monomers from disparate PDB sources.

• Structural Surgery (Mutagenesis): Performing in-memory mutations and automatic side-chain repair.

• From PDB to Solvated Box: Automating the geometry and chemistry of your simulation box setup.

🧪 Analysis & Discovery

• Binding Pocket Isolation: Extracting active sites using advanced spatial selection strings.

• Trajectory Performance Analysis: Calculating stability (RMSD) for thousands of frames in record time.

• Big Data Trajectories: Handling massive H5MSM files with ultra-low latency.

🎨 Interaction & Visualization

• Spectacular Visualizations: Mastering NGLView and MolSysViewer for publication-quality renders.

• Form Teleportation: Bridging MolSysMT with OpenMM, MDAnalysis, NetworkX, and BioPython.

• Ready for Simulation (OpenMM): The complete pipeline from experimental structure to GPU-ready simulation.

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