Your guide to YASARA View

°  Getting started °  The ten magic words °  Atom - YASARA's representation of a true atom °  Residue - any continuous stretch of atoms sharing the same residue name, residue number and molecule name °  Molecule - any continuous stretch of residues sharing the same molecule name °  Object - a collection of molecules and additional items °  Soup - all atoms in active objects °  Scene - all objects together °  All - the scene or the soup °  Bond - a covalent link between two atoms with pH dependent order °  Local coordinate system - The coordinate system within one object °  Global coordinate system - The coordinate system of the scene °  The three potential pitfalls °  You never get less than you want °  There is a difference between 'Hide', 'Switch off', 'Remove' and 'Delete' °  Gaps in a molecule are bridged by default °  The keys and mouse buttons to use °  Moving objects around °  Changing the scene style °  Editing °  Analyzing the soup °  Controlling a simulation °  Using the console °  Other keys °  The command line parameters °  Running YASARA in special environments °  Running YASARA without graphics °  Running YASARA on one machine with multiple users °  Running YASARA from an NFS mounted volume °  Running YASARA on a 64 bit operating system °  Working with extremely large protein structures °  Citing YASARA, its algorithms and force fields °  Reporting bugs, problems and inconveniences °  Screenshots as examples of what you can do