How-to guides# Task-oriented recipes. Each page solves one concrete problem and is self-contained. I/O# How to read a structure How to write a structure How to read a trajectory Selection and manipulation# How to select atoms How to filter and remove atoms How to append and merge molecules How to set and get properties Bonds, segments, topology# How to guess bonds How to assign segments and chains How to wrap trajectories Geometry and analysis# How to align structures How to compute distances and contacts How to compute dihedrals How to compute RMSD and RMSF Projections and interactions# How to compute projections How to compute protein–ligand interactions Conversion to other toolkits# How to convert a Molecule to RDKit or OpenFF Visualization# How to view a molecule External resources# How to fetch from RCSB and OPM
