User Guide# Get Started Installation Prerequisites Installation Optional Dependencies DTS Simulations DTS Backmapping Instructions for Developers Getting Help Quickstart Tutorials Influenza A Virus Requirements Visual Demonstration Membrane Segmentation Mesh Creation Clean the Segmentation Generate Initial Mesh Refine the Mesh Equilibrate the Mesh HMFF Simulation Constrained Template Matching Generate Seed Points Template Matching Refine Protein Picks Coarse-Grained Martini Models Backmapping Coarse Graining Equilibration References Working with in situ data Segmentation Connected Components Refinement Clustering Envelope Extraction Leiden Clustering Meshing Batch Processing Requirements Creating a Processing Pipeline Configuring Input Files Choosing Parameters Execution Settings Running the Pipeline Cluster Execution Reviewing Results Using Seed Points for Template Matching Pipeline Operations Reference Input Preprocessing Parametrization Export Troubleshooting Scripting Interface Getting Started Loading Data Inspecting Data Targeting Geometries Transient Results Command Substitution Organizing Results Analysis Filtering Sessions Putting It Together Scripts UI Reference Interface UI Layout Object Browser Context Menu Properties Dialog Status Bar Interaction Mode Interaction Target Processing Indicator Coordinate System Auxiliary Panels Volume Viewer Trajectory Player Next Steps File Operations Import Export Sessions Saving Sessions Loading Sessions Screenshots Animations Programmatic Access for Developers Tabs Segmentation Merge Remove Select by Size Transform Crop Cluster Outlier Removal Normals Trim Skeletonize Downsample Properties Parametrization Parametric Fitting Sphere Ellipsoid Cylinder Non-Parametric Fitting RBF (Radial Basis Function) Mesh Curve Sampling Operations Sample Mesh Operations Repair Remesh Smooth Project Fill Next Steps Intelligence Equilibrate HMFF Trajectory Backmapping Detection Template Match Membrane Reference File Formats Volume Formats MRC (.mrc, .map) EM (.em) HDF5 (.h5) Point Cloud Formats CSV (.csv, .xyz) TSV (.tsv) PDB (.pdb) GRO (.gro) STAR (.star) CIF (.cif) Mesh Formats OBJ (.obj) PLY (.ply) STL (.stl) Trajectory Formats TSI (.tsi, .q) VTU (.vtu) Session Format Pickle (.pickle) See Also Troubleshooting File Import Errors Performance Issues Selection Problems Crashes During Operations Export Failures Missing Features in Exported Files Session Won’t Load Mesh Generation Failures Issues License