Your guide to YASARA View

°  File - Load and save the scene or parts of it °  New scene - Start again °  PDB files - Load and save objects in plain PDB format °  YASARA objects - Load and save complete objects °  YASARA scenes - Load and save the entire scene °  OpenBabel - Import and export molecules using OpenBabel °  Screenshots - Save plain or ray-traced screenshots °  MPEG movies - Encode plain or ray-traced animations °  Simulation snapshots - Load and save simulation states °  Exit - Quit YASARA °  Edit - Change content and properties of the soup °  History - Undo and redo changes °  Objects - Center, transform, transfer, remove, add and delete °  Split points - Edit split points, split and join entire objects °  Bonds - Add, type and delete bonds °  Building - Build atoms to molecules, oligomers, crystals and loops °  Geometry - Set or optimize distances, angles and dihedrals °  Sampling - Search conformational space °  Surface environments - Define the context of surface analysis °  Hydrogens - Add, swap and delete °  Water - Delete all waters °  Names and numbers - Set or get properties of atoms to objects °  Simulation - Simulate the soup °  Preparing a simulation - Define and fill the cell °  Force fields - Get the recipe °  Simulation parameters - Choose your favorite ingredients °  Restraints - Enforce distances and dihedral angles °  Running a simulation - Keep the soup from boiling °  Analyze - Analyze the soup °  Atom position - Calculate average positions and RMSFs °  Superposition - Align atoms and calculate RMSDs °  Contacts - List contacts and hydrogen bonds °  Energy - Calculate energies °  Electrostatics - Calculate electrostatic potentials and charges °  Geometry - Measure distances, angles, dihedrals and radii °  Rotamers - Show rotamer distributions °  Secondary structure - Calculate secondary structure content °  Surface areas - Calculate VdW, molecular and accessible surfaces °  Volumes - Calculate VdW, molecular and solvent accessible volumes °  Soup content - List, count and compare units, get boundaries °  Checks - Search for errors °  View - Change the appearance of the soup °  Colors - Add a fourth dimension to your figures °  Visibility - Show and hide, switch on and off °  Style - Display atoms as balls, balls&sticks, sticks and traces °  Secondary structure - Show tubes, ribbons and cartoons °  Surfaces - Show VdW, molecular and solvent accessible surfaces °  Hydrogen bonds - Show hydrogen bonds °  Atoms - Choose atom styles °  Projection - Switch the perspective °  Lighting - Light the scene °  Effects - Change and animate the scene °  Position - Place and move objects °  Orientation - Orient and rotate objects °  Labels - Display text labels °  Marks and zooms - Mark atoms with fireflies and zoom in °  Arrows - Show arrows connecting atoms or points °  Solids - Show spheres, boxes, pyramids, cylinders, tori and others °  Images - Show and animate bitmaps °  Text - Print text, possibly in 3D letters °  Options - Other commands °  Experiments - Let YASARA cook for you °  Macros - Watch YASARA do the work for you °  Tables - Collect, visualize and export data °  Formats - Choose the residue output format °  Logs - Redirect output to a file °  Plugins - Run plugins from a macro °  Default pH - Set the H+ ion concentration and residue pKas °  Quantum mechanics - Configure YAPAC °  Coordinate system - Live in a left or right handed world °  Units - Choose your favorite units °  Parallel computations - Configure multi CPU core usage °  Input devices - Configure the interaction with YASARA °  Shell - Execute shell commands °  Window - Change the display properties °  Location - Place the YASARA window °  Menus - Change the appearance of menus °  Console - Configure the console °  Antialiasing - Smooth is better °  Frequency - Change the frames per second and save battery power °  Stereo - Time to touch your molecules °  Help - Access the documentation and solve problems °  Manual - Browse the HTML documentation °  Installation - Download missing programs °  Index - All commands in alphabetic order