Your guide to YASARA View

°  Run molecular dynamics simulations °  Preparing the topology °  Preparing the force field °  Deriving new (Y)AMBER force field parameters °  Deriving new NOVA force field parameters °  Running a simulation °  Analyzing a trajectory °  Playing back a trajectory °  Refine a homology model °  The quick method: in vacuo energy minimization with the NOVA force field °  The slow method: explicit solvent molecular dynamics simulation with the YAMBER force field °  Solve an NMR structure °  Setting the parameters °  Folding the structure °  Refining the structure in vacuo °  Refining the structure in explicit solvent °  Analyzing the ensemble °  Handling special cases like Cys-bridges, oligomers and metalloproteins °  Avoiding problems with hydrogen nomenclature °  Making floating assignments °  Create your own YASARA Movies °  Movies are written in Yanaconda °  Movies are stored in the yasara/mov directory °  Movies start with typical commands °  Movies can wait for a specified time or until you press a button °  Labels allow to jump back and forth between movie sections °  Work with YASARA and your text editor in parallel °  Movies can be imported from OpenOffice or PowerPoint °  Bitmap images can be displayed and animated °  Text can be displayed using 3D letters °  The look of the movie depends on the aspect ratio of the YASARA window °  Hints for using movies in important presentations