| | 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 |
|
|
