plotIntensityResolutionBinPlus.json

{
  "display_name": "plotIntensityResolutionBin",
  "metadata": {
    "language": "python",
    "description": "Miller arrays to plot of bin mean intensity over dstar",
    "tags": [
    "python","plotIntensityResolutionBin","iotbx","extra crystal symmetry"
    ],
    "code": [
      "'''",
      "from iotbx.file_reader import any_file",
      "import matplotlib.pyplot as plt",
      "",
      "f = any_file("${1:/Users/blaine/manuscripts/RETkinaseLoxo/ret_blu.mtz}")",
      "",
      "print(f.file_type)",
      "f.show_summary()",
      "miller_arrays = f.file_server.miller_arrays",
      "iobs =  miller_arrays[3]",
      "flags = miller_arrays[0]",
      "iobs, flags = iobs.common_sets(other=flags)",
      "iobsData = iobs.data()",
      "list(iobsData[100:110])",
      "iobs.show_comprehensive_summary()",
      "# iobs.binner()",
      "n_bins = ${2:20}",
      "binner = iobs.setup_binner(n_bins=n_bins)",
      "binner.show_summary()",
      "",
      "used = list(binner.range_used())",
      "selections = [binner.selection(i) for i in used]",
      "means = [iobs.select(sel).mean() for sel in selections]",
      "",
      "from math import log",
      "lnmeans = [log(y) for y in means]",
      "",
      "d_star_power = 1.618034",
      "centers = binner.bin_centers(d_star_power)",
      "d_centers = list(centers**(-1 / d_star_power))",
      "d_centers",
      "",
      "# plt.ylabel("Natural log of the amplitudes squared")",
      "# plt.xlabel(r"$\textrm{d^*}$ in $\textrm{\AA}$")",
      "# ax.set_xlim(35, 1.5)",
      "# plt.scatter(d_centers,lnmeanss)",
      "",
      "fig, ax = plt.subplots()",
      "ax.scatter(d_centers,lnmeans)",
      "ax.set_xlim(${3:8}, ${4:1.5})  # decreasing",
      "ax.set_xlabel(r"$d^*$ in $\AA$")",
      "ax.set_ylabel("Natural log of the intensities")",
      "ax.grid(False)",
      "plt.savefig("${5:iobsvsdstar}.pdf")",
      "$0'''",
      ""
      "from iotbx.file_reader import any_file",
      "import matplotlib.pyplot as plt",
      "",
      "f = any_file('/Users/blaine/manuscripts/RETkinaseLoxo/ret_blu.mtz')",
      "",
      "print(f.file_type)",
      "f.show_summary()",
      "miller_arrays = f.file_server.miller_arrays",
      "iobs =  miller_arrays[3]",
      "flags = miller_arrays[0]",
      "iobs, flags = iobs.common_sets(other=flags)",
      "iobsData = iobs.data()",
      "list(iobsData[100:110])",
      "iobs.show_comprehensive_summary()",
      "# iobs.binner()",
      "n_bins = 20",
      "binner = iobs.setup_binner(n_bins=n_bins)",
      "binner.show_summary()",
      "",
      "used = list(binner.range_used())",
      "selections = [binner.selection(i) for i in used]",
      "means = [iobs.select(sel).mean() for sel in selections]",
      "",
      "from math import log",
      "lnmeans = [log(y) for y in means]",
      "",
      "d_star_power = 1.618034",
      "centers = binner.bin_centers(d_star_power)",
      "d_centers = list(centers**(-1 / d_star_power))",
      "d_centers",
      "",
      "# plt.ylabel('Natural log of the amplitudes squared')",
      "# plt.xlabel(r'$\textrm{d^*$ in $\textrm{\AA$')",
      "# ax.set_xlim(35, 1.5)",
      "# plt.scatter(d_centers,lnmeanss)",
      "",
      "fig, ax = plt.subplots()",
      "ax.scatter(d_centers,lnmeans)",
      "ax.set_xlim(8, 1.5)  # decreasing",
      "ax.set_xlabel(r'$d^*$ in $\AA$')",
      "ax.set_ylabel('Natural log of the intensities')",
      "ax.grid(False)",
      "plt.savefig('iobsvsdstar.pdf')"
    ]
  },
  "schema_name": "code-snippet"
}