Endonuclease PvuII (1PVI) DNA - GATTACAGATTACA
CAP - Catabolite gene Activating Protein (1BER)
DNA - GATTACAGATTACAGATTACA Endonuclease PvuII bound to palindromic DNA recognition site CAGCTG (1PVI) DNA - GATTACAGATTACAGATTACA TBP - TATA box Binding Protein (1C9B)
CAP - Catabolite gene Activating Protein (1BER)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
TBP - TATA box Binding Protein (1C9B)
 

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Atom descriptors identify selected atoms

Atom descriptors are instances of the class atom_descriptor. Typically, you loop over all atom descriptors in the ith selection menu:


for j in range(yasara.selection[i].atoms):
  atom=yasara.selection[i].atom[j]

And then access various atom properties: 
atom.name
The name of the atom
atom.namespaced
The name of the atom including spaces (always four characters) 
atom.altloc
The alternate location indicator of the atom
atom.position
The position of the atom, a list with three cartesian coordinates 
atom.occupancy
The occupancy field of the atom in the original PDB file 
atom.bfactor
The B-factor of the atom
atom.number.inyas
The unique number/ID of the atom in YASARA (a string).
atom.number.inall
The sequential number of the atom in the soup (a string, starting with 1, the same as .inyas).
atom.number.inobj
The sequential number of the atom in the object (a string, starting with 1, usually the same number as in the PDB file).
atom.number.inmol
The sequential number of the atom in the molecule (a string, starting with 1).
atom.number.inres
The sequential number of the atom in the residue (a string, starting with 1).
atom.object
The object descriptor for the object the atom belongs to.
atom.molecule
The molecule descriptor for the molecule the atom belongs to.
atom.residue
The residue descriptor for the residue the atom belongs to.

You could then color the atom green: 

  yasara.ColorAtom(atom.number.inyas+",Green")

Or delete the entire residue the atom belongs to: 

  yasara.DelRes(atom.residue.number.inyas)