## selection() — create a new selection

`selection(*atoms)`

> This creates a new empty `selection` object. An initial group of atoms or other objects can be added to the selection by listing them here; see Section 6.9 for more information.

Example: examples/python/selection.py

      from modeller import *

      env = environ()
      env.io.atom_files_directory = ['../atom_files']
      env.libs.topology.read(file='$(LIB)/top_heav.lib')
      env.libs.parameters.read(file='$(LIB)/par.lib')

      mdl = model(env, file='1fdn')

      # New empty selection
      s = selection()

      # Add all atoms from residues 4 through 10 (chain A) inclusive (PDB numbering)
      s.add(mdl.residue_range('4:A', '10:A'))

      # Selection of all atoms currently within 5A of atom CA in residue 1 in chain A
      # (this destroys the previous selection):
      s = mdl.atoms['CA:1:A'].select_sphere(5)

      # Is the CB:1:A atom in the selection?
      print(mdl.atoms['CB:1:A'] in s)

      # Alternative ways of selecting the same atom:
      print(mdl.chains['A'].residues['1'].atoms['CB'] in s)
      print(mdl.residues['1:A'].atoms['CB'] in s)

      # All atoms currently within 5A of atom CA:1:A, OR currently within 3A of the
      # point (1,10,1):
      s = mdl.atoms['CA:1:A'].select_sphere(5) | mdl.point(1,10,1).select_sphere(3)

      # All atoms currently within 5A of atom CA:1:A, AND also currently within 3A
      # of the point (1,10,1):
      s = mdl.atoms['CA:1:A'].select_sphere(5) & mdl.point(1,10,1).select_sphere(3)

      # All atoms currently within 5A of atom CA:1:A, OR currently within 3A of the
      # point (1,10,1), but not BOTH:
      s = mdl.atoms['CA:1:A'].select_sphere(5) ^ mdl.point(1,10,1).select_sphere(3)

      # Create a selection containing the CA atom from residue 1, chain A,
      # and all of residue 2 (PDB numbering)
      s = selection(mdl.atoms['CA:1:A'], mdl.residues['2:A'])

      # All residues EXCEPT 5-10 in chain A (i.e. all atom selection minus the
      # selection of residues 5-10, otherwise known as an inverted selection):
      s = selection(mdl) - selection(mdl.residue_range('5:A', '10:A'))

      # All atoms in any residue that contains a CG atom
      s = selection(mdl).only_atom_types('CG').by_residue()

      # The same as above, plus all atoms in residues immediately neighboring
      # these residues (by sequence)
      s = selection(mdl).only_atom_types('CG').extend_by_residue(1)

      # Selection of residues 1, 4, 8 and 10-15 (PDB numbering) from chain A:
      s = selection(mdl.residues['1:A'], mdl.residues['4:A'], mdl.residues['8:A'],
                    mdl.residue_range('10:A', '15:A'))

      # Print the center of mass (note: not mass weighted)
      print(s.mass_center)

      # Rotate by 90 degrees about the z axis through the origin (0,0,0)
      # (right handed rotation)
      s.rotate_origin([0,0,1], 90)

      # The same thing, except that the axis passes through the center of mass:
      s.rotate_mass_center([0,0,1], 90)

      # Translate by 5 angstroms along the x axis
      s.translate([5.0, 0, 0])

      # Equivalent (but less efficient, as it involves calculating the COM)
      s.x += 5.0

Example: examples/commands/pick_atoms.py

      # This will pick various subsets of atoms in the MODEL and compare them
      # with MODEL2.

      from modeller import *

      env = environ()
      env.io.atom_files_directory = ['../atom_files']
      log.level(1, 1, 1, 1, 0)

      # Read the models and the alignment:
      mdl  = model(env, file='1fas')
      mdl2 = model(env, file='2ctx')
      aln = alignment(env, file='toxin.ali', align_codes=('1fas', '2ctx'))
      aln.write(file='toxin.pap', alignment_format='PAP')

      # Pick and superpose mainchain atoms:
      atmsel = selection(mdl).only_mainchain()
      atmsel.superpose(mdl2, aln)

      # Pick and superpose sidechain atoms:
      atmsel = selection(mdl).only_sidechain()
      atmsel.superpose(mdl2, aln)

      # Pick and superpose CA and CB atoms:
      atmsel = selection(mdl).only_atom_types('CA CB')
      atmsel.superpose(mdl2, aln)

      # Pick all atoms in residues with rings:
      atmsel = selection(mdl).only_residue_types('TYR PHE TRP HIS')

      # Pick and superpose all atoms:
      atmsel = selection(mdl)
      atmsel.superpose(mdl2, aln)

      # Pick and superpose CA and CB atoms in one segment only:
      atmsel = selection(mdl.residue_range('2:A', '10:A')).only_atom_types('CA CB')
      atmsel.superpose(mdl2, aln)

      # Pick and superpose all atoms within 6 angstroms of the 'CA' atom in
      # residue '10' in chain A:
      atmsel = mdl.atoms['CA:10:A'].select_sphere(6.0)
      atmsel.superpose(mdl2, aln)

      # Pick and superpose all atoms within 6 angstroms of any atom in
      # segment 2:A to 10:A
      atmsel = selection(mdl.residue_range('2:A', '10:A')).select_sphere(6.0)
      atmsel.superpose(mdl2, aln)

      # Pick all atoms in the model
      atmsel = selection(mdl)

      # Pick all atoms in all loops (ie residues within 2 positions
      # of any gap in the alignment):
      loops = mdl2.loops(aln, minlength=5, maxlength=15, insertion_ext=2,
                         deletion_ext=2)
      atmsel = selection(loops)

      # Pick all atoms within 6 angstroms of all loops
      atmsel = selection(loops).select_sphere(6.0)