°  'Element' switches to a selection of chemical elements You can select chemical elements by their one/two letter abbreviation, their full name or their number in the periodic table. Examples: ColorAtom Element H Carbon 8,Red Color atoms that are hydrogens or carbons or oxygens red DelAtom Element 1 Delete all hydrogen atoms ColorRes Element S,Blue Color all residues containing a sulfur atom blue DelAtom Element C-O Delete all carbon, nitrogen and oxygen atoms °  'SecStr' switches to a selection of secondary structure types After switching to the 'SecStr' selection type, use the keywords 'Strand', 'Helix', 'Turn' or 'Coil'. Examples: ColorRes SecStr Helix,Red Color all residues in a helix red ColorRes SecStr Turn Coil,Gray Color all residues in turn or coil gray DelMol SecStr Strand Delete all molecules that contain a strand °  'Segment' switches to a selection of macromolecular segments The PDB format reserves four characters in columns 73-76 to specify a segment ID, e.g. to distinguish the light and heavy chains in antibodies. In old PDB files, the segment ID is often the same as the PDB ID. Examples: ColorMol Segment HEAV, Green Color all molecules belonging to segment 'HEAV' green ListRestAtom Segment " A",Distance List all NMR distance restraints involving atoms in segment A °  'AltLoc' switches to a selection of alternate conformations Sometimes a bunch of atoms (mostly side-chains) can be seen at two or more distinct locations in the X-ray density map. These atoms are then present multiple times in the PDB file, but with different 'alternate location (AltLoc) indicators'. The 'AltLoc' selection type allows to choose one of these multiple conformations. Examples: DelAtom AltLoc B Delete all atoms with an alternate location indicator 'B' DelAtom AltLoc B-Z Delete all atoms with AltLoc indicators B to Z °  'Protein', 'NucAcid' and 'HetGroup' immediately select proteins, nucleic acids and the rest Contrary to the previous selection types, these three do not require an actual selection afterwards. That's why they leave the selection type unaltered, nevertheless they perform an implicit logical AND like all the others above. Examples: DelMol NucAcid Delete all nucleic acid molecules DelAtom CA CB Protein Delete all atoms named CA or CB and belonging to a protein DelRes HetGroup Delete everything that is neither a protein nor a nucleic acid °  'Backbone', 'Sidechain' and 'Visible' immediately select backbone, side-chain and visible atoms Everthing said for 'Protein', 'NucAcid' and 'HetGroup' also applies to these three. Note that the 'visible' selector looks at the atom visibilities set with Show and Hide , not at the object visibilities set with Switch . Examples: ColorAtom Sidechain,Blue Color all side-chain atoms blue ColorAtom Res Glu Asp Backbone,Red Color the backbone of Glu or Asp residues red DelRes Sidechain Delete all residues with a side-chain (no glycines) ShowSurfAtom O Res HOH visible,VdW Show a Van der Waals surface for all visible water oxygens DelAtom !visible Delete all invisible atoms °  'PDB', 'PDBRev', 'YASARA', 'IUPAC' and 'XPLOR' change the atom naming scheme Over the last decades, slightly different atom naming schemes have been introduced. For example YASARA and XPLOR name the terminal oxygens OT1 and OT2 to indicate their chemical equivalence, while the PDB prefers O and OXT, and IUPAC suggests O' and O''. If you are working in NMR spectroscopy, you are also used to the many problems associated with hydrogen nomenclature, which are described in more detail here. The operators described here allow to change the current naming scheme when selecting atoms. The new scheme stays valid until the next change or the next explicit operator. In the latter case, it is changed back to YASARA's own default names. Examples: ColorAtom PDB 1HB,blue Color the first of all equivalent beta-hydrogens blue ColorAtom XPLOR HB2,yellow Color all atoms whose XPLOR name is HB2 yellow DelAtom IUPAC HG3 PDB 1HB Delete atoms whose IUPAC name is HG3 plus those whose PDB name is 1HB DelAtom PDB OXT Delete all terminal oxygens ListAtom PDB 1HG and XPLOR HG2 List the first of all gamma-methylene hydrogen pairs °  'LocalX|Y|Z<>X' and 'GlobalX|Y|Z<>X' select atoms by their position Sometimes it is helpful to select atoms by their position, for example to slice a protein open and show only the back half. In YASARA, every atom has actually two positions, first the position in the local coordinate system of the object (which is specified in the PDB file), and second the position in the global coordinate system of the screen. Like those in the previous sections, the operators described here perform an implicit logical 'and'. Examples: HideAtom localX<0 Hide atoms with an X-position < 0 in the local coordinate system ShowAtom localY>5 localZ<-10 Show atoms with a local Y-position > 5 and a local Z-position < -10 HideAtom globalY<0 Hide atoms with a Y-position < 0 in the global coordinate system HideAtom globalX>0 Hide atoms in the right half of the screen °  'BFactor<>X', 'Occupancy<>X' and 'Property<>X' select atoms by B-factor, occupancy and property value In addition to coloring by BFactor , Occupancy and Property value, you can also use them to select atoms. Examples: CountAtom BFactor>60 Count the number of very flexible atoms DelAtom Occupancy<0.5 Delete all atoms with an occupancy smaller than 50% HideAtom Property=0 Hide all atoms whose property value is zero °  'Charge<=>X' selects units by their charge The Charge selection operator sums up the net charge of each unit (depending the current selection type) and selects those units that pass the comparison. If a force field has been initialized, the force field charge is used, otherwise YASARA resorts to the formal charge calculated from bond orders and standard atom valences. Examples: ListAtom Charge<0 List all atoms with a negative charge ColorRes Charge!=0,red Color all charged residues red ListRes Asp Glu Charge=0 List all aspartates and glutamates that are neutral ColorObj Charge>0,yellow Color all objects with a positive net charge yellow