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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.
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
# 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)