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