plotDstarsMeasurability.json

{
  "display_name": "plotDstarsMeasurability",
  "metadata": {
    "language": "python",
    "description": "Generate the list of dstars and measurability as lists for plotting by matplotlib.",
    "tags": [
    "python","plotDstarsMeasurability","iotbx","extra crystal symmetry"
    ],
    "code": [
      "from iotbx.reflection_file_reader import any_reflection_file",
      "hkl_file = any_reflection_file('3hz7.mtz')",
      "miller_arrays = hkl_file.as_miller_arrays(merge_equivalents=False)",
      "",
      "Iobs = miller_arrays[1]",
      "# Set up the bins",
      "n_bins = 50",
      "binner = Iobs.setup_binner(n_bins=n_bins)",
      "# binner.show_summary()",
      "used = list(binner.range_used())",
      "selections = [binner.selection(i) for i in used]",
      "",
      "# make d_centers for the x-axis",
      "d_star_power = 1.618034",
      "centers = binner.bin_centers(d_star_power)",
      "d_centers = list(centers**(-1 / d_star_power))",
      "",
      "# make list of the measurabilities by resolution bin",
      "meas = [Iobs.select(sel).measurability() for sel in selections]",
      "",
      "%matplotlib inline",
      "import matplotlib.pyplot as plt",
      "import matplotlib as mpl",
      "mpl.rcParams['savefig.dpi'] = 600",
      "mpl.rcParams['figure.dpi'] = 600",
      "",
      "fig, ax = plt.subplots(figsize=[3.25, 2.])",
      "ax.scatter(d_centers,lnmeans,c='k',alpha=0.3,s=5.5)",
      "",
      "ax.set_xlim(8, 1.5) # decreasing time",
      "ax.set_xlabel(r'$d^*$ in $\AA$',fontsize=12)",
      "ax.set_ylabel('ln(I)',fontsize=12)",
      "plt.xticks(fontsize=12)",
      "plt.yticks(fontsize=12)",
      "ax.grid(False)",
      "plt.savefig('3hz7measureability.pdf',bbox_inches='tight')",
      "plt.show()"
    ]
  },
  "schema_name": "code-snippet"
}