Your guide to YASARA View

°  Selections are defined by a final type and an expression °  Possible final selection types are All, Obj, Mol, Res and Atom °  Ranges can be specified with a minus sign °  A logical OR is assumed between items of the same selection type °  A logical AND is assumed if you switch the selection type °  Selections are inflated to the final selection type at the end °  Additional selection types allow to filter for various properties °  'Element' switches to a selection of chemical elements °  'SecStr' switches to a selection of secondary structure types °  'Segment' switches to a selection of macromolecular segments °  'AltLoc' switches to a selection of alternate conformations °  'Protein', 'NucAcid' and 'HetGroup' immediately select proteins, nucleic acids and the rest °  'Backbone', 'Sidechain' and 'Visible' immediately select backbone, side-chain and visible atoms °  'PDB', 'PDBRev', 'YASARA', 'IUPAC' and 'XPLOR' change the atom naming scheme °  'LocalX|Y|Z<>X' and 'GlobalX|Y|Z<>X' select atoms by their position °  'BFactor<>X', 'Occupancy<>X' and 'Property<>X' select atoms by B-factor, occupancy and property value °  'Charge<=>X' selects units by their charge °  Names can be negated with an exclamation mark '!' °  Names can be wildcards using a question mark '?' °  Names with unusual characters can be quoted °  Selections can be combined with explicit operators °  The 'and', 'or' and 'not' operators perform logical operations °  The 'with distance <>X from' operator measures distances between atoms °  The 'with minimum distance from' operator finds the closest atom °  The 'with maximum distance from' operator finds the most distant atom °  The 'with <>X atoms closer Y among' operator counts close atoms °  The 'with <>X bonds to' operator analyzes bound atoms °  The 'with <>X bond angles to' operator analyzes second neighbor atoms °  The 'with distance <>X from Y surface...' operator measures distances from a surface °  The 'with contribution to X surface...' operator analyzes surface contributions °  The 'within sequence' operator selects within a given sequence °  Selections are not case sensitive except for two special cases °  Selection windows allow to build selections with the mouse °  Yanaconda helps to define selection subsets °  Examples of selections needed in real-life