Example #1
0
def exercise2():
  pdb_in = iotbx.pdb.hierarchy.input(pdb_string="""\
ATOM   3988  P    DA G  10       2.095 -23.407  14.671  1.00 24.76           P
ATOM   3989  OP1  DA G  10       2.702 -22.768  13.479  1.00 24.54           O
ATOM   3990  OP2  DA G  10       1.098 -22.688  15.497  1.00 26.02           O
ATOM   3991  O5'  DA G  10       3.272 -23.890  15.629  1.00 22.57           O
ATOM   3992  C5'  DA G  10       2.981 -24.494  16.871  1.00 21.71           C
ATOM   3993  C4'  DA G  10       4.289 -24.903  17.501  1.00 21.29           C
ATOM   3994  O4'  DA G  10       4.850 -25.979  16.721  1.00 20.23           O
ATOM   3995  C3'  DA G  10       5.340 -23.803  17.483  1.00 20.46           C
ATOM   3996  O3'  DA G  10       5.492 -23.313  18.807  1.00 20.49           O
ATOM   3997  C2'  DA G  10       6.602 -24.471  16.925  1.00 18.76           C
ATOM   3998  C1'  DA G  10       6.243 -25.951  16.910  1.00 17.49           C
ATOM   3999  N9   DA G  10       6.839 -26.749  15.842  1.00 14.88           N
ATOM   4000  C8   DA G  10       6.713 -26.565  14.492  1.00 15.01           C
ATOM   4001  N7   DA G  10       7.363 -27.452  13.774  1.00 15.05           N
ATOM   4002  C5   DA G  10       7.945 -28.283  14.718  1.00 13.74           C
ATOM   4003  C6   DA G  10       8.766 -29.426  14.610  1.00 12.94           C
ATOM   4004  N6   DA G  10       9.149 -29.944  13.443  1.00 13.28           N
ATOM   4005  N1   DA G  10       9.181 -30.024  15.746  1.00 12.16           N
ATOM   4006  C2   DA G  10       8.797 -29.503  16.921  1.00 14.06           C
ATOM   4007  N3   DA G  10       8.029 -28.435  17.152  1.00 13.57           N
ATOM   4008  C4   DA G  10       7.629 -27.865  15.998  1.00 13.67           C
""")
  #open("tmp1.pdb", "w").write(pdb_in.hierarchy.as_pdb_string())
  base = pdb_in.hierarchy.only_atom_group()
  xyz = base.atoms().extract_xyz().deep_copy()
  flipbase.flip_base(base, angle=180)
  xyz_new = base.atoms().extract_xyz()
  assert approx_equal(xyz_new.rms_difference(xyz), 2.45942)
Example #2
0
def exercise2():
    pdb_in = iotbx.pdb.hierarchy.input(
        pdb_string="""\
ATOM   3988  P    DA G  10       2.095 -23.407  14.671  1.00 24.76           P
ATOM   3989  OP1  DA G  10       2.702 -22.768  13.479  1.00 24.54           O
ATOM   3990  OP2  DA G  10       1.098 -22.688  15.497  1.00 26.02           O
ATOM   3991  O5'  DA G  10       3.272 -23.890  15.629  1.00 22.57           O
ATOM   3992  C5'  DA G  10       2.981 -24.494  16.871  1.00 21.71           C
ATOM   3993  C4'  DA G  10       4.289 -24.903  17.501  1.00 21.29           C
ATOM   3994  O4'  DA G  10       4.850 -25.979  16.721  1.00 20.23           O
ATOM   3995  C3'  DA G  10       5.340 -23.803  17.483  1.00 20.46           C
ATOM   3996  O3'  DA G  10       5.492 -23.313  18.807  1.00 20.49           O
ATOM   3997  C2'  DA G  10       6.602 -24.471  16.925  1.00 18.76           C
ATOM   3998  C1'  DA G  10       6.243 -25.951  16.910  1.00 17.49           C
ATOM   3999  N9   DA G  10       6.839 -26.749  15.842  1.00 14.88           N
ATOM   4000  C8   DA G  10       6.713 -26.565  14.492  1.00 15.01           C
ATOM   4001  N7   DA G  10       7.363 -27.452  13.774  1.00 15.05           N
ATOM   4002  C5   DA G  10       7.945 -28.283  14.718  1.00 13.74           C
ATOM   4003  C6   DA G  10       8.766 -29.426  14.610  1.00 12.94           C
ATOM   4004  N6   DA G  10       9.149 -29.944  13.443  1.00 13.28           N
ATOM   4005  N1   DA G  10       9.181 -30.024  15.746  1.00 12.16           N
ATOM   4006  C2   DA G  10       8.797 -29.503  16.921  1.00 14.06           C
ATOM   4007  N3   DA G  10       8.029 -28.435  17.152  1.00 13.57           N
ATOM   4008  C4   DA G  10       7.629 -27.865  15.998  1.00 13.67           C
"""
    )
    # open("tmp1.pdb", "w").write(pdb_in.hierarchy.as_pdb_string())
    base = pdb_in.hierarchy.only_atom_group()
    xyz = base.atoms().extract_xyz().deep_copy()
    flipbase.flip_base(base, angle=180)
    xyz_new = base.atoms().extract_xyz()
    assert approx_equal(xyz_new.rms_difference(xyz), 2.45942)
Example #3
0
def exercise():
  """
  Exercise refine "easy" with DNA/RNA.
  """
  pi_good = get_pdb_inputs(pdb_str=pdb_str_answer, restraints=False)
  map_data = get_map(xrs=pi_good.xrs)
  xrs_good = pi_good.xrs.deep_copy_scatterers()
  pi_good.ph.write_pdb_file(file_name="answer.pdb",
    crystal_symmetry=xrs_good.crystal_symmetry())
  #
  pi_poor = get_pdb_inputs(pdb_str=pdb_str_poor, restraints=True)
  pi_poor.ph.write_pdb_file(file_name="poor.pdb")
  xrs_poor = pi_poor.xrs.deep_copy_scatterers()
  #
  d = xrs_good.distances(other=xrs_poor)
  print d.min_max_mean().as_tuple()
  assert flex.max(d)>3
  assert flex.mean(d)>1

  chain = 'B'
  res_num = 40
  alt_loc = None
  ero = False
  n_refine_cycles = 3
  target_map = get_map(xrs=pi_good.xrs)
  sites_cart = xrs_poor.sites_cart()
  for ch in pi_poor.ph.chains():
    if ch.id.strip() != chain : continue
    print 'chain'
    for rg in ch.residue_groups():
      if rg.resseq_as_int() != res_num : continue
      print "res#"
      if rg.have_conformers() and not alt_loc :
        s = 'Specified residue has alternate conformations. Please specify '
        raise RuntimeError(s + 'alt_loc on the command line')
      for residue in rg.atom_groups():
        if alt_loc and alt_loc != residue.altloc.strip():
          continue
        flipbase.flip_base(residue, angle=180)

        sites_cart.set_selected(residue.atoms().extract_i_seq(),
          residue.atoms().extract_xyz())
        xray_structure = xrs_poor.replace_sites_cart(sites_cart)
        sele = residue.atoms().extract_i_seq()
        print 'real-space refinement BEGIN'.center(79,'*')
        for i in range(n_refine_cycles):
          print 'real-space refinement cycle %i...' % (i + 1)
          ero = individual_sites.easy(
            map_data                    = target_map,
            xray_structure              = xray_structure,
            pdb_hierarchy               = pi_poor.ph,
            geometry_restraints_manager = pi_poor.grm,
            selection                   = sele)
        print 'real-space refinement FINISHED'.center(79,'*')
        xrs_refined = ero.xray_structure
  if not ero : raise RuntimeError('Specified residue not found')
  d = xrs_good.distances(other=xrs_refined)
  print d.min_max_mean().as_tuple()
  assert flex.max(d)<0.07
  assert flex.mean(d)<0.03
  ero.pdb_hierarchy.write_pdb_file(file_name="refined.pdb",
    crystal_symmetry=xrs_good.crystal_symmetry())
Example #4
0
def exercise():
    """
  Exercise refine "easy" with DNA/RNA.
  """
    pi_good = get_pdb_inputs(pdb_str=pdb_str_answer, restraints=False)
    map_data = get_map(xrs=pi_good.xrs)
    xrs_good = pi_good.xrs.deep_copy_scatterers()
    pi_good.ph.write_pdb_file(file_name="answer.pdb", crystal_symmetry=xrs_good.crystal_symmetry())
    #
    pi_poor = get_pdb_inputs(pdb_str=pdb_str_poor, restraints=True)
    pi_poor.ph.write_pdb_file(file_name="poor.pdb")
    xrs_poor = pi_poor.xrs.deep_copy_scatterers()
    #
    d = xrs_good.distances(other=xrs_poor)
    print d.min_max_mean().as_tuple()
    assert flex.max(d) > 3
    assert flex.mean(d) > 1

    chain = "B"
    res_num = 40
    alt_loc = None
    ero = False
    n_refine_cycles = 3
    target_map = get_map(xrs=pi_good.xrs)
    sites_cart = xrs_poor.sites_cart()
    for ch in pi_poor.ph.chains():
        if ch.id.strip() != chain:
            continue
        print "chain"
        for rg in ch.residue_groups():
            if rg.resseq_as_int() != res_num:
                continue
            print "res#"
            if rg.have_conformers() and not alt_loc:
                s = "Specified residue has alternate conformations. Please specify "
                raise RuntimeError(s + "alt_loc on the command line")
            for residue in rg.atom_groups():
                if alt_loc and alt_loc != residue.altloc.strip():
                    continue
                flipbase.flip_base(residue, angle=180)

                sites_cart.set_selected(residue.atoms().extract_i_seq(), residue.atoms().extract_xyz())
                xray_structure = xrs_poor.replace_sites_cart(sites_cart)
                sele = residue.atoms().extract_i_seq()
                print "real-space refinement BEGIN".center(79, "*")
                for i in range(n_refine_cycles):
                    print "real-space refinement cycle %i..." % (i + 1)
                    ero = individual_sites.easy(
                        map_data=target_map,
                        xray_structure=xray_structure,
                        pdb_hierarchy=pi_poor.ph,
                        geometry_restraints_manager=pi_poor.grm,
                        selection=sele,
                    )
                print "real-space refinement FINISHED".center(79, "*")
                xrs_refined = ero.xray_structure
    if not ero:
        raise RuntimeError("Specified residue not found")
    d = xrs_good.distances(other=xrs_refined)
    print d.min_max_mean().as_tuple()
    assert flex.max(d) < 0.07
    assert flex.mean(d) < 0.03
    ero.pdb_hierarchy.write_pdb_file(file_name="refined.pdb", crystal_symmetry=xrs_good.crystal_symmetry())