{ "cells": [ { "cell_type": "code", "execution_count": 61, "metadata": {}, "outputs": [], "source": [ "import matplotlib.pyplot as plt # to start\n", "import pandas as pd\n", "import matplotlib.pyplot as plt\n", "%matplotlib inline\n", "plt.style.use('classic')\n", "import numpy as np\n", "\n", "\"\"\"version when the same protein gets SMD2_2 and SMD2_1\"\"\"\n", "\n", "f = \"/Users/magnus/work/spliceosome/PyMOL4Spliceosome/bucket/rna-tools/rna_tools/tools/PyMOL4RNA/Spliceosome_PyMOL.xlsx\"\n", "df = pd.read_excel(f)\n", "path = '/Users/magnus/work/src/rna-tools/rna_tools/tools/PyMOL4RNA/'\n", "\n", "# ok, this is a list of [, , ]\n", "strucs = [\n", " ['S1_B_5zwo', '5zwo', '_B5zwo'],\n", " ['S2_Bact_5gm6', '5gm6', '_Ba5gm6'],\n", " ['S3_C_5lj3', '5lj3', '_C5lj3'],\n", " ['S4_Cstar_5mps', '5mps', '_Cs5mps'],\n", " ['S5_P_6exn', '6exn', '_P6exn'],\n", " ['S5_P_5ylz', '5ylz', '_P5ylz'],\n", " ['S6_ILS_5y88', '5y88', '_I5y88'],\n", " ['SX_pX_3jb9', '3jb9', '_3jb9'],\n", " ['S6_hP_6icz', '6icz', '_hP_6icz'],\n", " ['hBa_6ff7', '6ff7', '_hBa_6ff7'],\n", " ['hC_5yzg', '5yzg', '_hC_5yzg'],\n", " ['hX_5xjc', '5xjc', '_hX_5xjc'],\n", " ['y3_5gan', '5gan', '_y3_5gan'],\n", " ['h3_6qw6', '6qw6', '_h3_6qw6'],\n", " ['h3_3jcr', '3jcr', '_h3_3jcr'],\n", " ['h3_6qx9', '6qx9', '_h3_6qx9'],\n", " ['h_Bpre_6ah0', '6ah0', '_h_Bp_6ah0'],\n", " ] \n", "strs = []\n", "for s in strucs:\n", " strs.append(s[1])\n", "strs = str(strs) #strs = \"['5gm6', '5zwo', '5lj3', '5gm6', '5mps', '6exn', '5ylz', '5y88', '3jb9', '6icz']\"" ] }, { "cell_type": "code", "execution_count": 62, "metadata": { "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "try:\n", " from pymol import cmd\n", "except ImportError:\n", " print(\"PyMOL Python lib is missing\")\n", " # sys.exit(0)\n", "\n", "def spl_extract():\n", " for name in cmd.get_names(\"all\"):\n", " #if name in ['5zwo', '5gm6', '5lj3', '5mps', '6exn', '5ylz', '5y88', '3jb9', '6icz', '6ff7', '5yzg', '5xjc', '5gan', '6qw6', '3jcr', '6qx9', '6ah0']: # this should be auto\n", " print(\" \\ Extracting mode for %s\" % name)\n", "\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '5zwo' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '5zwo' in name.lower():\n", " cmd.extract(\"PRP8_B5zwo\", \"chain A and \" + object_name)\n", " cmd.extract(\"BRR2_B5zwo\", \"chain D and \" + object_name)\n", " cmd.extract(\"LEA1_B5zwo\", \"chain o and \" + object_name)\n", " cmd.extract(\"Msl1_B5zwo\", \"chain p and \" + object_name)\n", " cmd.extract(\"SNU114_B5zwo\", \"chain C and \" + object_name)\n", " cmd.extract(\"U2_B5zwo\", \"chain H and \" + object_name)\n", " cmd.extract(\"U5_B5zwo\", \"chain B and \" + object_name)\n", " cmd.extract(\"U6_B5zwo\", \"chain F and \" + object_name)\n", " cmd.extract(\"U4_B5zwo\", \"chain I and \" + object_name)\n", " cmd.extract(\"Intron_B5zwo\", \"chain G and \" + object_name)\n", " cmd.extract(\"PRP4_B5zwo\", \"chain K and \" + object_name)\n", " cmd.extract(\"PRP31_B5zwo\", \"chain L and \" + object_name)\n", " cmd.extract(\"PRP6_B5zwo\", \"chain N and \" + object_name)\n", " cmd.extract(\"PRP3_B5zwo\", \"chain J and \" + object_name)\n", " cmd.extract(\"DIB1_B5zwo\", \"chain E and \" + object_name)\n", " cmd.extract(\"SNU13_B5zwo\", \"chain M and \" + object_name)\n", " cmd.extract(\"LSM8_B5zwo\", \"chain z and \" + object_name)\n", " cmd.extract(\"LSM2_B5zwo\", \"chain q and \" + object_name)\n", " cmd.extract(\"LSM3_B5zwo\", \"chain r and \" + object_name)\n", " cmd.extract(\"LSM6_B5zwo\", \"chain x and \" + object_name)\n", " cmd.extract(\"LSM5_B5zwo\", \"chain t and \" + object_name)\n", " cmd.extract(\"LSM7_B5zwo\", \"chain y and \" + object_name)\n", " cmd.extract(\"LSM4_B5zwo\", \"chain s and \" + object_name)\n", " cmd.extract(\"SNU66_B5zwo\", \"chain O and \" + object_name)\n", " cmd.extract(\"BUD13_B5zwo\", \"chain Y and \" + object_name)\n", " cmd.extract(\"Cus1_B5zwo\", \"chain 2 and \" + object_name)\n", " cmd.extract(\"HSH155_B5zwo\", \"chain 1 and \" + object_name)\n", " cmd.extract(\"HSH49_B5zwo\", \"chain 4 and \" + object_name)\n", " cmd.extract(\"PML1_B5zwo\", \"chain Z and \" + object_name)\n", " cmd.extract(\"PRP11_B5zwo\", \"chain v and \" + object_name)\n", " cmd.extract(\"RDS3_B5zwo\", \"chain 5 and \" + object_name)\n", " cmd.extract(\"RSE1_B5zwo\", \"chain 3 and \" + object_name)\n", " cmd.extract(\"SNU17_B5zwo\", \"chain X and \" + object_name)\n", " cmd.extract(\"Ysf3_B5zwo\", \"chain 6 and \" + object_name)\n", " cmd.extract(\"SMB1_1_B5zwo\", \"chain a and \" + object_name)\n", " cmd.extract(\"SMB1_2_B5zwo\", \"chain P and \" + object_name)\n", " cmd.extract(\"SMB1_3_B5zwo\", \"chain h and \" + object_name)\n", " cmd.extract(\"SME1_1_B5zwo\", \"chain e and \" + object_name)\n", " cmd.extract(\"SME1_2_B5zwo\", \"chain T and \" + object_name)\n", " cmd.extract(\"SME1_3_B5zwo\", \"chain i and \" + object_name)\n", " cmd.extract(\"SMX3_1_B5zwo\", \"chain f and \" + object_name)\n", " cmd.extract(\"SMX3_2_B5zwo\", \"chain U and \" + object_name)\n", " cmd.extract(\"SMX3_3_B5zwo\", \"chain j and \" + object_name)\n", " cmd.extract(\"SMX2_1_B5zwo\", \"chain g and \" + object_name)\n", " cmd.extract(\"SMX2_2_B5zwo\", \"chain V and \" + object_name)\n", " cmd.extract(\"SMX2_3_B5zwo\", \"chain k and \" + object_name)\n", " cmd.extract(\"SMD3_1_B5zwo\", \"chain d and \" + object_name)\n", " cmd.extract(\"SMD3_2_B5zwo\", \"chain S and \" + object_name)\n", " cmd.extract(\"SMD3_3_B5zwo\", \"chain l and \" + object_name)\n", " cmd.extract(\"SMD1_1_B5zwo\", \"chain b and \" + object_name)\n", " cmd.extract(\"SMD1_2_B5zwo\", \"chain Q and \" + object_name)\n", " cmd.extract(\"SMD1_3_B5zwo\", \"chain m and \" + object_name)\n", " cmd.extract(\"SMD2_1_B5zwo\", \"chain c and \" + object_name)\n", " cmd.extract(\"SMD2_2_B5zwo\", \"chain R and \" + object_name)\n", " cmd.extract(\"SMD2_3_B5zwo\", \"chain n and \" + object_name)\n", " cmd.extract(\"PRP9_B5zwo\", \"chain u and \" + object_name)\n", " cmd.extract(\"PRP21_B5zwo\", \"chain w and \" + object_name)\n", " cmd.extract(\"SNU23_B5zwo\", \"chain W and \" + object_name)\n", " cmd.extract(\"PRP38_B5zwo\", \"chain 0 and \" + object_name)\n", " cmd.extract(\"SPP381_B5zwo\", \"chain 9 and \" + object_name)\n", " cmd.set_name(object_name, \"unknown_other_B5zwo\")\n", " cmd.group(\"B5zwo\", \"*_B5zwo\")\n", " cmd.do(\"order *, yes\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '5gm6' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '5gm6' in name.lower():\n", " cmd.extract(\"PRP8_Ba5gm6\", \"chain A and \" + object_name)\n", " cmd.extract(\"BRR2_Ba5gm6\", \"chain B and \" + object_name)\n", " cmd.extract(\"BUD31_Ba5gm6\", \"chain T and \" + object_name)\n", " cmd.extract(\"CEF1_Ba5gm6\", \"chain c and \" + object_name)\n", " cmd.extract(\"CWC15_Ba5gm6\", \"chain S and \" + object_name)\n", " cmd.extract(\"CWC2_hRBM22_Ba5gm6\", \"chain R and \" + object_name)\n", " cmd.extract(\"CWC21_Ba5gm6\", \"chain X and \" + object_name)\n", " cmd.extract(\"CWC22_Ba5gm6\", \"chain Z and \" + object_name)\n", " cmd.extract(\"PRP45_Ba5gm6\", \"chain P and \" + object_name)\n", " cmd.extract(\"CDC40_Ba5gm6\", \"chain n and \" + object_name)\n", " cmd.extract(\"PRP19_Ba5gm6\", \"chain f and \" + object_name)\n", " cmd.extract(\"PRP46_Ba5gm6\", \"chain O and \" + object_name)\n", " cmd.extract(\"SLT11/ECM2_Ba5gm6\", \"chain Q and \" + object_name)\n", " cmd.extract(\"SNT309_Ba5gm6\", \"chain t and \" + object_name)\n", " cmd.extract(\"SNU114_Ba5gm6\", \"chain C and \" + object_name)\n", " cmd.extract(\"SYF2_Ba5gm6\", \"chain f and \" + object_name)\n", " cmd.extract(\"SYF1_Ba5gm6\", \"chain v and \" + object_name)\n", " cmd.extract(\"U2_Ba5gm6\", \"chain 2 and \" + object_name)\n", " cmd.extract(\"U5_Ba5gm6\", \"chain 5 and \" + object_name)\n", " cmd.extract(\"U6_Ba5gm6\", \"chain 6 and \" + object_name)\n", " cmd.extract(\"Intron_Ba5gm6\", \"chain M and \" + object_name)\n", " cmd.extract(\"Exon_Ba5gm6\", \"chain N and \" + object_name)\n", " cmd.extract(\"BUD13_Ba5gm6\", \"chain W and \" + object_name)\n", " cmd.extract(\"CLF2_Ba5gm6\", \"chain d and \" + object_name)\n", " cmd.extract(\"Cus1_Ba5gm6\", \"chain H and \" + object_name)\n", " cmd.extract(\"CWC24_Ba5gm6\", \"chain a and \" + object_name)\n", " cmd.extract(\"CWC27_Ba5gm6\", \"chain b and \" + object_name)\n", " cmd.extract(\"HSH155_Ba5gm6\", \"chain G and \" + object_name)\n", " cmd.extract(\"HSH49_Ba5gm6\", \"chain e and \" + object_name)\n", " cmd.extract(\"PML1_Ba5gm6\", \"chain U and \" + object_name)\n", " cmd.extract(\"PRP11_Ba5gm6\", \"chain I and \" + object_name)\n", " cmd.extract(\"PRP2_Ba5gm6\", \"chain Y and \" + object_name)\n", " cmd.extract(\"RDS3_Ba5gm6\", \"chain J and \" + object_name)\n", " cmd.extract(\"RSE1_Ba5gm6\", \"chain F and \" + object_name)\n", " cmd.extract(\"SNU17_Ba5gm6\", \"chain V and \" + object_name)\n", " cmd.extract(\"Ysf3_Ba5gm6\", \"chain K and \" + object_name)\n", " cmd.set_name(object_name, \"unknown_other_Ba5gm6\")\n", " cmd.group(\"Ba5gm6\", \"*_Ba5gm6\")\n", " cmd.do(\"order *, yes\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '5lj3' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '5lj3' in name.lower():\n", " cmd.extract(\"PRP8_C5lj3\", \"chain A and \" + object_name)\n", " cmd.extract(\"BUD31_C5lj3\", \"chain L and \" + object_name)\n", " cmd.extract(\"CEF1_C5lj3\", \"chain O and \" + object_name)\n", " cmd.extract(\"CLF1_C5lj3\", \"chain S and \" + object_name)\n", " cmd.extract(\"CWC15_C5lj3\", \"chain P and \" + object_name)\n", " cmd.extract(\"CWC16/YJU2_C5lj3\", \"chain D and \" + object_name)\n", " cmd.extract(\"CWC2_hRBM22_C5lj3\", \"chain M and \" + object_name)\n", " cmd.extract(\"CWC21_C5lj3\", \"chain R and \" + object_name)\n", " cmd.extract(\"CWC22_C5lj3\", \"chain H and \" + object_name)\n", " cmd.extract(\"CWC25_C5lj3\", \"chain F and \" + object_name)\n", " cmd.extract(\"ISY1_C5lj3\", \"chain G and \" + object_name)\n", " cmd.extract(\"LEA1_C5lj3\", \"chain W and \" + object_name)\n", " cmd.extract(\"Msl1_C5lj3\", \"chain Y and \" + object_name)\n", " cmd.extract(\"PRP45_C5lj3\", \"chain K and \" + object_name)\n", " cmd.extract(\"PRP46_C5lj3\", \"chain J and \" + object_name)\n", " cmd.extract(\"SLT11/ECM2_C5lj3\", \"chain N and \" + object_name)\n", " cmd.extract(\"SNU114_C5lj3\", \"chain C and \" + object_name)\n", " cmd.extract(\"SYF1_C5lj3\", \"chain T and \" + object_name)\n", " cmd.extract(\"U2_C5lj3\", \"chain Z and \" + object_name)\n", " cmd.extract(\"U5_C5lj3\", \"chain U and \" + object_name)\n", " cmd.extract(\"U6_C5lj3\", \"chain V and \" + object_name)\n", " cmd.extract(\"Intron_C5lj3\", \"chain I and \" + object_name)\n", " cmd.extract(\"Exon_C5lj3\", \"chain E and \" + object_name)\n", " cmd.extract(\"SMB1_1_C5lj3\", \"chain b and \" + object_name)\n", " cmd.extract(\"SMB1_2_C5lj3\", \"chain k and \" + object_name)\n", " cmd.extract(\"SME1_1_C5lj3\", \"chain e and \" + object_name)\n", " cmd.extract(\"SME1_2_C5lj3\", \"chain p and \" + object_name)\n", " cmd.extract(\"SMX3_1_C5lj3\", \"chain f and \" + object_name)\n", " cmd.extract(\"SMX3_2_C5lj3\", \"chain q and \" + object_name)\n", " cmd.extract(\"SMX2_1_C5lj3\", \"chain g and \" + object_name)\n", " cmd.extract(\"SMX2_2_C5lj3\", \"chain r and \" + object_name)\n", " cmd.extract(\"SMD3_1_C5lj3\", \"chain d and \" + object_name)\n", " cmd.extract(\"SMD3_2_C5lj3\", \"chain n and \" + object_name)\n", " cmd.extract(\"SMD1_1_C5lj3\", \"chain h and \" + object_name)\n", " cmd.extract(\"SMD1_2_C5lj3\", \"chain l and \" + object_name)\n", " cmd.extract(\"SMD2_1_C5lj3\", \"chain j and \" + object_name)\n", " cmd.extract(\"SMD2_2_C5lj3\", \"chain m and \" + object_name)\n", " cmd.set_name(object_name, \"unknown_other_C5lj3\")\n", " cmd.group(\"C5lj3\", \"*_C5lj3\")\n", " cmd.do(\"order *, yes\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '5mps' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '5mps' in name.lower():\n", " cmd.extract(\"PRP8_Cs5mps\", \"chain A and \" + object_name)\n", " cmd.extract(\"BUD31_Cs5mps\", \"chain L and \" + object_name)\n", " cmd.extract(\"CEF1_Cs5mps\", \"chain O and \" + object_name)\n", " cmd.extract(\"CLF1_Cs5mps\", \"chain S and \" + object_name)\n", " cmd.extract(\"CWC15_Cs5mps\", \"chain P and \" + object_name)\n", " cmd.extract(\"CWC2_hRBM22_Cs5mps\", \"chain M and \" + object_name)\n", " cmd.extract(\"CWC21_Cs5mps\", \"chain R and \" + object_name)\n", " cmd.extract(\"CWC22_Cs5mps\", \"chain H and \" + object_name)\n", " cmd.extract(\"PRP45_Cs5mps\", \"chain K and \" + object_name)\n", " cmd.extract(\"CDC40_Cs5mps\", \"chain o and \" + object_name)\n", " cmd.extract(\"PRP46_Cs5mps\", \"chain J and \" + object_name)\n", " cmd.extract(\"SLT11/ECM2_Cs5mps\", \"chain N and \" + object_name)\n", " cmd.extract(\"SNU114_Cs5mps\", \"chain C and \" + object_name)\n", " cmd.extract(\"SYF2_Cs5mps\", \"chain y and \" + object_name)\n", " cmd.extract(\"SYF1_Cs5mps\", \"chain T and \" + object_name)\n", " cmd.extract(\"U2_Cs5mps\", \"chain 2 and \" + object_name)\n", " cmd.extract(\"U5_Cs5mps\", \"chain 5 and \" + object_name)\n", " cmd.extract(\"U6_Cs5mps\", \"chain 6 and \" + object_name)\n", " cmd.extract(\"5EXON_Cs5mps\", \"chain E and \" + object_name)\n", " cmd.extract(\"Intron_Cs5mps\", \"chain I and \" + object_name)\n", " cmd.extract(\"Exon_Cs5mps\", \"chain E and \" + object_name)\n", " cmd.extract(\"SMB1_Cs5mps\", \"chain b and \" + object_name)\n", " cmd.extract(\"SME1_Cs5mps\", \"chain e and \" + object_name)\n", " cmd.extract(\"SMX3_Cs5mps\", \"chain f and \" + object_name)\n", " cmd.extract(\"SMX2_Cs5mps\", \"chain g and \" + object_name)\n", " cmd.extract(\"SMD3_Cs5mps\", \"chain d and \" + object_name)\n", " cmd.extract(\"SMD1_Cs5mps\", \"chain h and \" + object_name)\n", " cmd.extract(\"SMD2_Cs5mps\", \"chain j and \" + object_name)\n", " cmd.extract(\"PRP18_Cs5mps\", \"chain a and \" + object_name)\n", " cmd.extract(\"SLU7_Cs5mps\", \"chain c and \" + object_name)\n", " cmd.set_name(object_name, \"unknown_other_Cs5mps\")\n", " cmd.group(\"Cs5mps\", \"*_Cs5mps\")\n", " cmd.do(\"order *, yes\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '6exn' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '6exn' in name.lower():\n", " cmd.extract(\"PRP8_P6exn\", \"chain A and \" + object_name)\n", " cmd.extract(\"BUD31_P6exn\", \"chain L and \" + object_name)\n", " cmd.extract(\"CEF1_P6exn\", \"chain O and \" + object_name)\n", " cmd.extract(\"CLF1_P6exn\", \"chain S and \" + object_name)\n", " cmd.extract(\"CWC15_P6exn\", \"chain P and \" + object_name)\n", " cmd.extract(\"CWC16/YJU2_P6exn\", \"chain D and \" + object_name)\n", " cmd.extract(\"CWC2_hRBM22_P6exn\", \"chain M and \" + object_name)\n", " cmd.extract(\"CWC21_P6exn\", \"chain R and \" + object_name)\n", " cmd.extract(\"CWC22_P6exn\", \"chain H and \" + object_name)\n", " cmd.extract(\"LEA1_P6exn\", \"chain W and \" + object_name)\n", " cmd.extract(\"Msl1_P6exn\", \"chain Y and \" + object_name)\n", " cmd.extract(\"PRP45_P6exn\", \"chain K and \" + object_name)\n", " cmd.extract(\"CDC40_P6exn\", \"chain o and \" + object_name)\n", " cmd.extract(\"PRP19_1_P6exn\", \"chain t and \" + object_name)\n", " cmd.extract(\"PRP19_2_P6exn\", \"chain u and \" + object_name)\n", " cmd.extract(\"PRP19_3_P6exn\", \"chain v and \" + object_name)\n", " cmd.extract(\"PRP19_4_P6exn\", \"chain w and \" + object_name)\n", " cmd.extract(\"PRP46_P6exn\", \"chain J and \" + object_name)\n", " cmd.extract(\"SLT11/ECM2_P6exn\", \"chain N and \" + object_name)\n", " cmd.extract(\"SNU114_P6exn\", \"chain C and \" + object_name)\n", " cmd.extract(\"SYF1_P6exn\", \"chain T and \" + object_name)\n", " cmd.extract(\"U2_P6exn\", \"chain 2 and \" + object_name)\n", " cmd.extract(\"U5_P6exn\", \"chain 5 and \" + object_name)\n", " cmd.extract(\"U6_P6exn\", \"chain 6 and \" + object_name)\n", " cmd.extract(\"Intron_P6exn\", \"chain I and \" + object_name)\n", " cmd.extract(\"Exon_P6exn\", \"chain E and \" + object_name)\n", " cmd.extract(\"SMB1_1_P6exn\", \"chain b and \" + object_name)\n", " cmd.extract(\"SMB1_2_P6exn\", \"chain k and \" + object_name)\n", " cmd.extract(\"SME1_1_P6exn\", \"chain e and \" + object_name)\n", " cmd.extract(\"SME1_2_P6exn\", \"chain p and \" + object_name)\n", " cmd.extract(\"SMX3_1_P6exn\", \"chain f and \" + object_name)\n", " cmd.extract(\"SMX3_2_P6exn\", \"chain q and \" + object_name)\n", " cmd.extract(\"SMX2_1_P6exn\", \"chain g and \" + object_name)\n", " cmd.extract(\"SMX2_2_P6exn\", \"chain r and \" + object_name)\n", " cmd.extract(\"SMD3_1_P6exn\", \"chain d and \" + object_name)\n", " cmd.extract(\"SMD3_2_P6exn\", \"chain n and \" + object_name)\n", " cmd.extract(\"SMD1_1_P6exn\", \"chain h and \" + object_name)\n", " cmd.extract(\"SMD1_2_P6exn\", \"chain l and \" + object_name)\n", " cmd.extract(\"SMD2_1_P6exn\", \"chain j and \" + object_name)\n", " cmd.extract(\"SMD2_2_P6exn\", \"chain m and \" + object_name)\n", " cmd.extract(\"PRP22_P6exn\", \"chain V and \" + object_name)\n", " cmd.extract(\"PRP18_P6exn\", \"chain a and \" + object_name)\n", " cmd.extract(\"SLU7_P6exn\", \"chain c and \" + object_name)\n", " cmd.extract(\"unassigned_P6exn\", \"chain X and \" + object_name)\n", " cmd.set_name(object_name, \"unknown_other_P6exn\")\n", " cmd.group(\"P6exn\", \"*_P6exn\")\n", " cmd.do(\"order *, yes\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '5ylz' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '5ylz' in name.lower():\n", " cmd.extract(\"PRP8_P5ylz\", \"chain A and \" + object_name)\n", " cmd.extract(\"BUD31_P5ylz\", \"chain L and \" + object_name)\n", " cmd.extract(\"CEF1_P5ylz\", \"chain J and \" + object_name)\n", " cmd.extract(\"CLF1_P5ylz\", \"chain I and \" + object_name)\n", " cmd.extract(\"CWC15_P5ylz\", \"chain P and \" + object_name)\n", " cmd.extract(\"CWC2_hRBM22_P5ylz\", \"chain N and \" + object_name)\n", " cmd.extract(\"CWC21_P5ylz\", \"chain R and \" + object_name)\n", " cmd.extract(\"CWC22_P5ylz\", \"chain S and \" + object_name)\n", " cmd.extract(\"LEA1_P5ylz\", \"chain o and \" + object_name)\n", " cmd.extract(\"Msl1_P5ylz\", \"chain p and \" + object_name)\n", " cmd.extract(\"PRP45_P5ylz\", \"chain Q and \" + object_name)\n", " cmd.extract(\"CDC40_P5ylz\", \"chain T and \" + object_name)\n", " cmd.extract(\"PRP19_1_P5ylz\", \"chain q and \" + object_name)\n", " cmd.extract(\"PRP19_2_P5ylz\", \"chain r and \" + object_name)\n", " cmd.extract(\"PRP19_3_P5ylz\", \"chain s and \" + object_name)\n", " cmd.extract(\"PRP19_4_P5ylz\", \"chain t and \" + object_name)\n", " cmd.extract(\"PRP46_P5ylz\", \"chain O and \" + object_name)\n", " cmd.extract(\"SLT11/ECM2_P5ylz\", \"chain M and \" + object_name)\n", " cmd.extract(\"SNT309_P5ylz\", \"chain G and \" + object_name)\n", " cmd.extract(\"SNU114_P5ylz\", \"chain C and \" + object_name)\n", " cmd.extract(\"SYF2_P5ylz\", \"chain K and \" + object_name)\n", " cmd.extract(\"SYF1_P5ylz\", \"chain H and \" + object_name)\n", " cmd.extract(\"U2_P5ylz\", \"chain F and \" + object_name)\n", " cmd.extract(\"U5_P5ylz\", \"chain B and \" + object_name)\n", " cmd.extract(\"U6_P5ylz\", \"chain D and \" + object_name)\n", " cmd.extract(\"Intron_P5ylz\", \"chain E and \" + object_name)\n", " cmd.extract(\"SMB1_1_P5ylz\", \"chain a and \" + object_name)\n", " cmd.extract(\"SMB1_2_P5ylz\", \"chain h and \" + object_name)\n", " cmd.extract(\"SME1_1_P5ylz\", \"chain b and \" + object_name)\n", " cmd.extract(\"SME1_2_P5ylz\", \"chain i and \" + object_name)\n", " cmd.extract(\"SMX3_1_P5ylz\", \"chain c and \" + object_name)\n", " cmd.extract(\"SMX3_2_P5ylz\", \"chain j and \" + object_name)\n", " cmd.extract(\"SMX2_1_P5ylz\", \"chain d and \" + object_name)\n", " cmd.extract(\"SMX2_2_P5ylz\", \"chain k and \" + object_name)\n", " cmd.extract(\"SMD3_1_P5ylz\", \"chain e and \" + object_name)\n", " cmd.extract(\"SMD3_2_P5ylz\", \"chain l and \" + object_name)\n", " cmd.extract(\"SMD1_1_P5ylz\", \"chain f and \" + object_name)\n", " cmd.extract(\"SMD1_2_P5ylz\", \"chain m and \" + object_name)\n", " cmd.extract(\"SMD2_1_P5ylz\", \"chain g and \" + object_name)\n", " cmd.extract(\"SMD2_2_P5ylz\", \"chain n and \" + object_name)\n", " cmd.extract(\"PRP22_P5ylz\", \"chain W and \" + object_name)\n", " cmd.extract(\"PRP18_P5ylz\", \"chain U and \" + object_name)\n", " cmd.extract(\"SLU7_P5ylz\", \"chain V and \" + object_name)\n", " cmd.set_name(object_name, \"unknown_other_P5ylz\")\n", " cmd.group(\"P5ylz\", \"*_P5ylz\")\n", " cmd.do(\"order *, yes\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '5y88' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '5y88' in name.lower():\n", " cmd.extract(\"PRP8_I5y88\", \"chain A and \" + object_name)\n", " cmd.extract(\"BUD31_I5y88\", \"chain L and \" + object_name)\n", " cmd.extract(\"CLF1_I5y88\", \"chain I and \" + object_name)\n", " cmd.extract(\"CWC15_I5y88\", \"chain P and \" + object_name)\n", " cmd.extract(\"CWC16/YJU2_I5y88\", \"chain R and \" + object_name)\n", " cmd.extract(\"CWC2_hRBM22_I5y88\", \"chain N and \" + object_name)\n", " cmd.extract(\"CWC25_I5y88\", \"chain G and \" + object_name)\n", " cmd.extract(\"Intron_2_I5y88\", \"chain E and \" + object_name)\n", " cmd.extract(\"LEA1_I5y88\", \"chain o and \" + object_name)\n", " cmd.extract(\"Msl1_I5y88\", \"chain p and \" + object_name)\n", " cmd.extract(\"PRP45_I5y88\", \"chain Q and \" + object_name)\n", " cmd.extract(\"CDC40_I5y88\", \"chain S and \" + object_name)\n", " cmd.extract(\"PRP19_1_I5y88\", \"chain q and \" + object_name)\n", " cmd.extract(\"PRP19_2_I5y88\", \"chain r and \" + object_name)\n", " cmd.extract(\"PRP19_3_I5y88\", \"chain s and \" + object_name)\n", " cmd.extract(\"PRP19_4_I5y88\", \"chain t and \" + object_name)\n", " cmd.extract(\"PRP46_I5y88\", \"chain O and \" + object_name)\n", " cmd.extract(\"SLT11/ECM2_I5y88\", \"chain M and \" + object_name)\n", " cmd.extract(\"SNT309_I5y88\", \"chain G and \" + object_name)\n", " cmd.extract(\"SNU114_I5y88\", \"chain C and \" + object_name)\n", " cmd.extract(\"SYF2_I5y88\", \"chain K and \" + object_name)\n", " cmd.extract(\"SYF1_I5y88\", \"chain H and \" + object_name)\n", " cmd.extract(\"U2_I5y88\", \"chain F and \" + object_name)\n", " cmd.extract(\"U5_I5y88\", \"chain B and \" + object_name)\n", " cmd.extract(\"U6_I5y88\", \"chain D and \" + object_name)\n", " cmd.extract(\"Intron_I5y88\", \"chain x and \" + object_name)\n", " cmd.extract(\"RNA_I5y88\", \"chain x and \" + object_name)\n", " cmd.extract(\"cwc23_I5y88\", \"chain T and \" + object_name)\n", " cmd.extract(\"SPP382_I5y88\", \"chain U and \" + object_name)\n", " cmd.extract(\"NTR2_I5y88\", \"chain V and \" + object_name)\n", " cmd.extract(\"PRP43_I5y88\", \"chain W and \" + object_name)\n", " cmd.extract(\"SMB1_1_I5y88\", \"chain a and \" + object_name)\n", " cmd.extract(\"SMB1_2_I5y88\", \"chain h and \" + object_name)\n", " cmd.extract(\"SME1_1_I5y88\", \"chain b and \" + object_name)\n", " cmd.extract(\"SME1_2_I5y88\", \"chain i and \" + object_name)\n", " cmd.extract(\"SMX3_1_I5y88\", \"chain c and \" + object_name)\n", " cmd.extract(\"SMX3_2_I5y88\", \"chain j and \" + object_name)\n", " cmd.extract(\"SMX2_1_I5y88\", \"chain d and \" + object_name)\n", " cmd.extract(\"SMX2_2_I5y88\", \"chain k and \" + object_name)\n", " cmd.extract(\"SMD3_1_I5y88\", \"chain e and \" + object_name)\n", " cmd.extract(\"SMD3_2_I5y88\", \"chain l and \" + object_name)\n", " cmd.extract(\"SMD1_1_I5y88\", \"chain f and \" + object_name)\n", " cmd.extract(\"SMD1_2_I5y88\", \"chain m and \" + object_name)\n", " cmd.extract(\"SMD2_1_I5y88\", \"chain g and \" + object_name)\n", " cmd.extract(\"SMD2_2_I5y88\", \"chain n and \" + object_name)\n", " cmd.set_name(object_name, \"unknown_other_I5y88\")\n", " cmd.group(\"I5y88\", \"*_I5y88\")\n", " cmd.do(\"order *, yes\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '3jb9' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '3jb9' in name.lower():\n", " cmd.extract(\"U2_3jb9\", \"chain P and \" + object_name)\n", " cmd.extract(\"U5_3jb9\", \"chain C and \" + object_name)\n", " cmd.extract(\"U6_3jb9\", \"chain N and \" + object_name)\n", " cmd.extract(\"Intron_1_3jb9\", \"chain O and \" + object_name)\n", " cmd.extract(\"Intron_2_3jb9\", \"chain Q and \" + object_name)\n", " cmd.extract(\"Spp42_yPrp8_3jb9\", \"chain A and \" + object_name)\n", " cmd.extract(\"CWF15_yCWC15_3jb9\", \"chain h and \" + object_name)\n", " cmd.set_name(object_name, \"unknown_other_3jb9\")\n", " cmd.group(\"3jb9\", \"*_3jb9\")\n", " cmd.do(\"order *, yes\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '6icz' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '6icz' in name.lower():\n", " cmd.extract(\"CWC15_hP_6icz\", \"chain P and \" + object_name)\n", " cmd.extract(\"U2_hP_6icz\", \"chain H and \" + object_name)\n", " cmd.extract(\"U5_hP_6icz\", \"chain B and \" + object_name)\n", " cmd.extract(\"U6_hP_6icz\", \"chain F and \" + object_name)\n", " cmd.extract(\"Intron_hP_6icz\", \"chain G and \" + object_name)\n", " cmd.extract(\"cwc23_hP_6icz\", \"chain 6ICZ and \" + object_name)\n", " cmd.set_name(object_name, \"unknown_other_hP_6icz\")\n", " cmd.group(\"hP_6icz\", \"*_hP_6icz\")\n", " cmd.do(\"order *, yes\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '6ff7' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '6ff7' in name.lower():\n", " cmd.extract(\"CWC15_hBa_6ff7\", \"chain R and \" + object_name)\n", " cmd.extract(\"CWC2_hRBM22_hBa_6ff7\", \"chain P and \" + object_name)\n", " cmd.extract(\"U2_hBa_6ff7\", \"chain 2 and \" + object_name)\n", " cmd.extract(\"U5_hBa_6ff7\", \"chain 5 and \" + object_name)\n", " cmd.extract(\"U6_hBa_6ff7\", \"chain 6 and \" + object_name)\n", " cmd.extract(\"Intron_hBa_6ff7\", \"chain Z and \" + object_name)\n", " cmd.set_name(object_name, \"unknown_other_hBa_6ff7\")\n", " cmd.group(\"hBa_6ff7\", \"*_hBa_6ff7\")\n", " cmd.do(\"order *, yes\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '5yzg' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '5yzg' in name.lower():\n", " cmd.extract(\"CWC15_hC_5yzg\", \"chain P and \" + object_name)\n", " cmd.extract(\"CWC2_hRBM22_hC_5yzg\", \"chain O and \" + object_name)\n", " cmd.extract(\"CWC25_hC_5yzg\", \"chain X and \" + object_name)\n", " cmd.extract(\"PRP16_hDHX38_hC_5yzg\", \"chain Z and \" + object_name)\n", " cmd.extract(\"U2_hC_5yzg\", \"chain H and \" + object_name)\n", " cmd.extract(\"U5_hC_5yzg\", \"chain B and \" + object_name)\n", " cmd.extract(\"U6_hC_5yzg\", \"chain F and \" + object_name)\n", " cmd.extract(\"Intron_hC_5yzg\", \"chain G and \" + object_name)\n", " cmd.set_name(object_name, \"unknown_other_hC_5yzg\")\n", " cmd.group(\"hC_5yzg\", \"*_hC_5yzg\")\n", " cmd.do(\"order *, yes\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '5xjc' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '5xjc' in name.lower():\n", " cmd.extract(\"CWC15_hX_5xjc\", \"chain P and \" + object_name)\n", " cmd.extract(\"CWC25_hX_5xjc\", \"chain X and \" + object_name)\n", " cmd.extract(\"U2_hX_5xjc\", \"chain H and \" + object_name)\n", " cmd.extract(\"U5_hX_5xjc\", \"chain B and \" + object_name)\n", " cmd.extract(\"U6_hX_5xjc\", \"chain F and \" + object_name)\n", " cmd.extract(\"Intron_hX_5xjc\", \"chain G and \" + object_name)\n", " cmd.extract(\"PRKRIP1_hX_5xjc\", \"chain X and \" + object_name)\n", " cmd.set_name(object_name, \"unknown_other_hX_5xjc\")\n", " cmd.group(\"hX_5xjc\", \"*_hX_5xjc\")\n", " cmd.do(\"order *, yes\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '5gan' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '5gan' in name.lower():\n", " cmd.extract(\"PRP8_y3_5gan\", \"chain A and \" + object_name)\n", " cmd.extract(\"BRR2_y3_5gan\", \"chain B and \" + object_name)\n", " cmd.extract(\"PRP45_y3_5gan\", \"chain H and \" + object_name)\n", " cmd.extract(\"SNU114_y3_5gan\", \"chain C and \" + object_name)\n", " cmd.extract(\"U5_y3_5gan\", \"chain U and \" + object_name)\n", " cmd.extract(\"U6_y3_5gan\", \"chain W and \" + object_name)\n", " cmd.extract(\"U4_y3_5gan\", \"chain V and \" + object_name)\n", " cmd.extract(\"PRP31_y3_5gan\", \"chain F and \" + object_name)\n", " cmd.extract(\"PRP6_y3_5gan\", \"chain J and \" + object_name)\n", " cmd.extract(\"PRP3_y3_5gan\", \"chain G and \" + object_name)\n", " cmd.extract(\"DIB1_y3_5gan\", \"chain D and \" + object_name)\n", " cmd.extract(\"SNU13_y3_5gan\", \"chain K and \" + object_name)\n", " cmd.extract(\"LSM8_y3_5gan\", \"chain 8 and \" + object_name)\n", " cmd.extract(\"LSM2_y3_5gan\", \"chain 2 and \" + object_name)\n", " cmd.extract(\"LSM3_y3_5gan\", \"chain 3 and \" + object_name)\n", " cmd.extract(\"LSM6_y3_5gan\", \"chain 6 and \" + object_name)\n", " cmd.extract(\"LSM5_y3_5gan\", \"chain 5 and \" + object_name)\n", " cmd.extract(\"LSM7_y3_5gan\", \"chain 7 and \" + object_name)\n", " cmd.extract(\"LSM4_y3_5gan\", \"chain 4 and \" + object_name)\n", " cmd.extract(\"SNU66_y3_5gan\", \"chain E and \" + object_name)\n", " cmd.extract(\"SMB1_1_y3_5gan\", \"chain b and \" + object_name)\n", " cmd.extract(\"SMB1_2_y3_5gan\", \"chain k and \" + object_name)\n", " cmd.extract(\"SME1_1_y3_5gan\", \"chain e and \" + object_name)\n", " cmd.extract(\"SME1_2_y3_5gan\", \"chain p and \" + object_name)\n", " cmd.extract(\"SMX3_1_y3_5gan\", \"chain f and \" + object_name)\n", " cmd.extract(\"SMX3_2_y3_5gan\", \"chain q and \" + object_name)\n", " cmd.extract(\"SMX2_1_y3_5gan\", \"chain g and \" + object_name)\n", " cmd.extract(\"SMX2_2_y3_5gan\", \"chain r and \" + object_name)\n", " cmd.extract(\"SMD3_1_y3_5gan\", \"chain d and \" + object_name)\n", " cmd.extract(\"SMD3_2_y3_5gan\", \"chain n and \" + object_name)\n", " cmd.extract(\"SMD1_1_y3_5gan\", \"chain h and \" + object_name)\n", " cmd.extract(\"SMD1_2_y3_5gan\", \"chain l and \" + object_name)\n", " cmd.extract(\"SMD2_1_y3_5gan\", \"chain j and \" + object_name)\n", " cmd.extract(\"SMD2_2_y3_5gan\", \"chain m and \" + object_name)\n", " cmd.extract(\"unassigned_y3_5gan\", \"chain X and \" + object_name)\n", " cmd.set_name(object_name, \"unknown_other_y3_5gan\")\n", " cmd.group(\"y3_5gan\", \"*_y3_5gan\")\n", " cmd.do(\"order *, yes\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '6qw6' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '6qw6' in name.lower():\n", " cmd.extract(\"PRP8_h3_6qw6\", \"chain 5A and \" + object_name)\n", " cmd.extract(\"U5_h3_6qw6\", \"chain 5 and \" + object_name)\n", " cmd.extract(\"U6_h3_6qw6\", \"chain 6 and \" + object_name)\n", " cmd.extract(\"U4_h3_6qw6\", \"chain 4 and \" + object_name)\n", " cmd.extract(\"Prp28_h3_6qw6\", \"chain 5X and \" + object_name)\n", " cmd.set_name(object_name, \"unknown_other_h3_6qw6\")\n", " cmd.group(\"h3_6qw6\", \"*_h3_6qw6\")\n", " cmd.do(\"order *, yes\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '3jcr' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '3jcr' in name.lower():\n", " cmd.extract(\"PRP8_h3_3jcr\", \"chain A and \" + object_name)\n", " cmd.extract(\"BRR2_h3_3jcr\", \"chain C and \" + object_name)\n", " cmd.extract(\"SNU114_h3_3jcr\", \"chain B and \" + object_name)\n", " cmd.extract(\"U5_h3_3jcr\", \"chain H and \" + object_name)\n", " cmd.extract(\"U6_h3_3jcr\", \"chain N and \" + object_name)\n", " cmd.extract(\"U4_h3_3jcr\", \"chain M and \" + object_name)\n", " cmd.extract(\"PRP4_h3_3jcr\", \"chain L and \" + object_name)\n", " cmd.extract(\"PRP31_h3_3jcr\", \"chain J and \" + object_name)\n", " cmd.extract(\"PRP6_h3_3jcr\", \"chain G and \" + object_name)\n", " cmd.extract(\"PRP3_h3_3jcr\", \"chain K and \" + object_name)\n", " cmd.extract(\"SNU13_h3_3jcr\", \"chain I and \" + object_name)\n", " cmd.extract(\"LSM8_h3_3jcr\", \"chain 8 and \" + object_name)\n", " cmd.extract(\"LSM2_h3_3jcr\", \"chain 2 and \" + object_name)\n", " cmd.extract(\"LSM3_h3_3jcr\", \"chain 3 and \" + object_name)\n", " cmd.extract(\"LSM5_h3_3jcr\", \"chain 5 and \" + object_name)\n", " cmd.extract(\"LSM7_h3_3jcr\", \"chain 7 and \" + object_name)\n", " cmd.extract(\"LSM4_h3_3jcr\", \"chain 4 and \" + object_name)\n", " cmd.extract(\"SMD3_1_h3_3jcr\", \"chain R and \" + object_name)\n", " cmd.extract(\"SMD3_2_h3_3jcr\", \"chain r and \" + object_name)\n", " cmd.extract(\"SMD1_1_h3_3jcr\", \"chain P and \" + object_name)\n", " cmd.extract(\"SMD1_2_h3_3jcr\", \"chain p and \" + object_name)\n", " cmd.extract(\"SMD2_1_h3_3jcr\", \"chain Q and \" + object_name)\n", " cmd.extract(\"SMD2_2_h3_3jcr\", \"chain q and \" + object_name)\n", " cmd.extract(\"U5-40K_h3_3jcr\", \"chain D and \" + object_name)\n", " cmd.extract(\"Dim1_h3_3jcr\", \"chain E and \" + object_name)\n", " cmd.extract(\"Prp28_h3_3jcr\", \"chain F and \" + object_name)\n", " cmd.extract(\"SmE_1_h3_3jcr\", \"chain S and \" + object_name)\n", " cmd.extract(\"SmE_2_h3_3jcr\", \"chain s and \" + object_name)\n", " cmd.extract(\"SmF_1_h3_3jcr\", \"chain T and \" + object_name)\n", " cmd.extract(\"SmF_2_h3_3jcr\", \"chain t and \" + object_name)\n", " cmd.extract(\"SmG_1_h3_3jcr\", \"chain U and \" + object_name)\n", " cmd.extract(\"SmG_2_h3_3jcr\", \"chain u and \" + object_name)\n", " cmd.extract(\"Sad1_h3_3jcr\", \"chain V and \" + object_name)\n", " cmd.extract(\"SmB_1_h3_3jcr\", \"chain O and \" + object_name)\n", " cmd.extract(\"SmB_2_h3_3jcr\", \"chain o and \" + object_name)\n", " cmd.set_name(object_name, \"unknown_other_h3_3jcr\")\n", " cmd.group(\"h3_3jcr\", \"*_h3_3jcr\")\n", " cmd.do(\"order *, yes\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '6qx9' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '6qx9' in name.lower():\n", " cmd.extract(\"PRP8_h3_6qx9\", \"chain 5A and \" + object_name)\n", " cmd.extract(\"U2_h3_6qx9\", \"chain 2 and \" + object_name)\n", " cmd.extract(\"U5_h3_6qx9\", \"chain 5 and \" + object_name)\n", " cmd.extract(\"U6_h3_6qx9\", \"chain 6 and \" + object_name)\n", " cmd.extract(\"U4_h3_6qx9\", \"chain 4 and \" + object_name)\n", " cmd.extract(\"Intron_h3_6qx9\", \"chain I and \" + object_name)\n", " cmd.extract(\"U1_h3_6qx9\", \"chain 1 and \" + object_name)\n", " cmd.extract(\"Prp28_h3_6qx9\", \"chain 5X and \" + object_name)\n", " cmd.set_name(object_name, \"unknown_other_h3_6qx9\")\n", " cmd.group(\"h3_6qx9\", \"*_h3_6qx9\")\n", " cmd.do(\"order *, yes\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '6ah0' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '6ah0' in name.lower():\n", " cmd.extract(\"PRP8_h_Bp_6ah0\", \"chain A and \" + object_name)\n", " cmd.extract(\"U2_h_Bp_6ah0\", \"chain H and \" + object_name)\n", " cmd.extract(\"U5_h_Bp_6ah0\", \"chain B and \" + object_name)\n", " cmd.extract(\"U6_h_Bp_6ah0\", \"chain F and \" + object_name)\n", " cmd.extract(\"U4_h_Bp_6ah0\", \"chain I and \" + object_name)\n", " cmd.extract(\"Intron_h_Bp_6ah0\", \"chain G and \" + object_name)\n", " cmd.extract(\"Prp28_h_Bp_6ah0\", \"chain X and \" + object_name)\n", " cmd.set_name(object_name, \"unknown_other_h_Bp_6ah0\")\n", " cmd.group(\"h_Bp_6ah0\", \"*_h_Bp_6ah0\")\n", " cmd.do(\"order *, yes\")\n", "\n" ] } ], "source": [ "#strucs = [['S3_C_5lj3', '5lj3']] # for debugging\n", "txt = \"\"\"\n", "try:\n", " from pymol import cmd\n", "except ImportError:\n", " print(\"PyMOL Python lib is missing\")\n", " # sys.exit(0)\n", "\n", "def spl_extract():\n", " for name in cmd.get_names(\"all\"):\n", " #if name in \"\"\" + strs + \"\"\": # this should be auto\n", " print(\" \\ Extracting mode for %s\" % name)\n", "\n", "\"\"\"\n", "\n", "for struc_col, pdb_id, complex_code in strucs:\n", " txt += \"\"\" \n", " for n in cmd.get_names(\"all\"):\n", " if '%s' in n:\n", " object_name = n\n", " print(object_name)\n", " \\n\"\"\" % pdb_id\n", " \n", " txt += \" if '\" + pdb_id + \"' in name.lower():\\n\"\n", " for index, i in df.iterrows():\n", " #print(i)\n", " ref = str(i['chain']).strip()\n", " struc = str(i[struc_col]).strip()\n", " # print(ref, struc)\n", " # todo fix cmd.extract(\"CDC40 (PRP17, SLU4, XRS2)\", \"chain n\")\n", " i['protein'] = i['protein'].split()[0]\n", " if struc != 'nan' and struc != '-': # if ref != 'nan' # i dont' use reference chain any more\n", " if ',' in struc:\n", " subchains = struc.split(',') # a,P,h\n", " for index , sc in enumerate(subchains): \n", " sc = sc.strip()\n", " # cmd.extract(name, selection, source_state, target_state)\n", " txt += ' cmd.extract(\"' + i['protein'] + '_' + str(index + 1) \\\n", " + complex_code + '\", \"chain ' + sc + ' and \" + object_name)\\n'\n", " # one mode to see these two proteins\n", " #print(' cmd.extract(\"' + i['protein'] + '\", \"chain ' + '+'.join(subchains) + '\")') \n", " else:\n", " #if ref != struc:\n", " txt += ' cmd.extract(\"' + i['protein'] + complex_code + '\", \"chain ' + struc + ' and \" + object_name)\\n'\n", " # the rest make unkown at the very end\n", " txt += ' cmd.set_name(object_name, \"unknown_other' + complex_code + '\")\\n'\n", " txt += ' cmd.group(\"' + complex_code[1:] + '\", \"*' + complex_code + '\")\\n' # this [1:] to get y3_5gan from _y3_5gan\n", " txt += ' cmd.do(\"order *, yes\")\\n'\n", "print(txt) \n", "with open(path + '/code_for_spl.py', 'w') as f:\n", " f.write(txt) " ] }, { "cell_type": "code", "execution_count": 63, "metadata": { "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "try:\n", " from pymol import cmd\n", "except ImportError:\n", " print(\"PyMOL Python lib is missing\")\n", " # sys.exit(0)\n", "\n", "def spl_color():\n", " for name in cmd.get_names(\"all\"):\n", " # cmd.do('color grey50') # off gray\n", " #if name in ['5zwo', '5gm6', '5lj3', '5mps', '6exn', '5ylz', '5y88', '3jb9', '6icz', '6ff7', '5yzg', '5xjc', '5gan', '6qw6', '3jcr', '6qx9', '6ah0']: # this should be auto\n", " print(\" \\ Extracting mode for %s\" % name)\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '5zwo' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '5zwo' in name.lower():\n", " #PRP8\n", " cmd.do(\"color skyblue, chain A and \" + object_name)\n", " cmd.do(\"color skyblue, PRP8_B5zwo\")\n", " #BRR2\n", " cmd.do(\"color grey60, chain D and \" + object_name)\n", " cmd.do(\"color grey60, BRR2_B5zwo\")\n", " #LEA1\n", " cmd.do(\"color palegreen, chain o and \" + object_name)\n", " cmd.do(\"color palegreen, LEA1_B5zwo\")\n", " #Msl1\n", " cmd.do(\"color palegreen, chain p and \" + object_name)\n", " cmd.do(\"color palegreen, Msl1_B5zwo\")\n", " #SNU114\n", " cmd.do(\"color slate, chain C and \" + object_name)\n", " cmd.do(\"color slate, SNU114_B5zwo\")\n", " #U2\n", " cmd.do(\"color forest, chain H and \" + object_name)\n", " cmd.do(\"color forest, U2_B5zwo\")\n", " #U5\n", " cmd.do(\"color density, chain B and \" + object_name)\n", " cmd.do(\"color density, U5_B5zwo\")\n", " #U6\n", " cmd.do(\"color firebrick, chain F and \" + object_name)\n", " cmd.do(\"color firebrick, U6_B5zwo\")\n", " #U4\n", " cmd.do(\"color brown, chain I and \" + object_name)\n", " cmd.do(\"color brown, U4_B5zwo\")\n", " #Intron\n", " cmd.do(\"color black, chain G and \" + object_name)\n", " cmd.do(\"color black, Intron_B5zwo\")\n", " #PRP4\n", " cmd.do(\"color grey50, chain K and \" + object_name)\n", " cmd.do(\"color grey50, PRP4_B5zwo\")\n", " #PRP31\n", " cmd.do(\"color grey50, chain L and \" + object_name)\n", " cmd.do(\"color grey50, PRP31_B5zwo\")\n", " #PRP6\n", " cmd.do(\"color grey50, chain N and \" + object_name)\n", " cmd.do(\"color grey50, PRP6_B5zwo\")\n", " #PRP3\n", " cmd.do(\"color grey50, chain J and \" + object_name)\n", " cmd.do(\"color grey50, PRP3_B5zwo\")\n", " #DIB1\n", " cmd.do(\"color grey50, chain E and \" + object_name)\n", " cmd.do(\"color grey50, DIB1_B5zwo\")\n", " #SNU13\n", " cmd.do(\"color grey50, chain M and \" + object_name)\n", " cmd.do(\"color grey50, SNU13_B5zwo\")\n", " #LSM8\n", " cmd.do(\"color grey50, chain z and \" + object_name)\n", " cmd.do(\"color grey50, LSM8_B5zwo\")\n", " #LSM2\n", " cmd.do(\"color grey50, chain q and \" + object_name)\n", " cmd.do(\"color grey50, LSM2_B5zwo\")\n", " #LSM3\n", " cmd.do(\"color grey50, chain r and \" + object_name)\n", " cmd.do(\"color grey50, LSM3_B5zwo\")\n", " #LSM6\n", " cmd.do(\"color grey50, chain x and \" + object_name)\n", " cmd.do(\"color grey50, LSM6_B5zwo\")\n", " #LSM5\n", " cmd.do(\"color grey50, chain t and \" + object_name)\n", " cmd.do(\"color grey50, LSM5_B5zwo\")\n", " #LSM7\n", " cmd.do(\"color grey50, chain y and \" + object_name)\n", " cmd.do(\"color grey50, LSM7_B5zwo\")\n", " #LSM4\n", " cmd.do(\"color grey50, chain s and \" + object_name)\n", " cmd.do(\"color grey50, LSM4_B5zwo\")\n", " #SNU66\n", " cmd.do(\"color grey50, chain O and \" + object_name)\n", " cmd.do(\"color grey50, SNU66_B5zwo\")\n", " #BUD13\n", " cmd.do(\"color grey60, chain Y and \" + object_name)\n", " cmd.do(\"color grey60, BUD13_B5zwo\")\n", " #Cus1\n", " cmd.do(\"color palegreen, chain 2 and \" + object_name)\n", " cmd.do(\"color palegreen, Cus1_B5zwo\")\n", " #HSH155\n", " cmd.do(\"color smudge, chain 1 and \" + object_name)\n", " cmd.do(\"color smudge, HSH155_B5zwo\")\n", " #HSH49\n", " cmd.do(\"color sand, chain 4 and \" + object_name)\n", " cmd.do(\"color sand, HSH49_B5zwo\")\n", " #PML1\n", " cmd.do(\"color grey60, chain Z and \" + object_name)\n", " cmd.do(\"color grey60, PML1_B5zwo\")\n", " #PRP11\n", " cmd.do(\"color palegreen, chain v and \" + object_name)\n", " cmd.do(\"color palegreen, PRP11_B5zwo\")\n", " #RDS3\n", " cmd.do(\"color palegreen, chain 5 and \" + object_name)\n", " cmd.do(\"color palegreen, RDS3_B5zwo\")\n", " #RSE1\n", " cmd.do(\"color smudge, chain 3 and \" + object_name)\n", " cmd.do(\"color smudge, RSE1_B5zwo\")\n", " #SNU17\n", " cmd.do(\"color grey60, chain X and \" + object_name)\n", " cmd.do(\"color grey60, SNU17_B5zwo\")\n", " #Ysf3\n", " cmd.do(\"color palegreen, chain 6 and \" + object_name)\n", " cmd.do(\"color palegreen, Ysf3_B5zwo\")\n", " cmd.do(\"color grey50, chain a and 5zwo\")\n", " cmd.do(\"color grey50, chain P and 5zwo\")\n", " cmd.do(\"color grey50, chain h and 5zwo\")\n", " cmd.do(\"color grey50, chain e and 5zwo\")\n", " cmd.do(\"color grey50, chain T and 5zwo\")\n", " cmd.do(\"color grey50, chain i and 5zwo\")\n", " cmd.do(\"color grey50, chain f and 5zwo\")\n", " cmd.do(\"color grey50, chain U and 5zwo\")\n", " cmd.do(\"color grey50, chain j and 5zwo\")\n", " cmd.do(\"color grey50, chain g and 5zwo\")\n", " cmd.do(\"color grey50, chain V and 5zwo\")\n", " cmd.do(\"color grey50, chain k and 5zwo\")\n", " cmd.do(\"color grey50, chain d and 5zwo\")\n", " cmd.do(\"color grey50, chain S and 5zwo\")\n", " cmd.do(\"color grey50, chain l and 5zwo\")\n", " cmd.do(\"color grey50, chain b and 5zwo\")\n", " cmd.do(\"color grey50, chain Q and 5zwo\")\n", " cmd.do(\"color grey50, chain m and 5zwo\")\n", " cmd.do(\"color grey50, chain c and 5zwo\")\n", " cmd.do(\"color grey50, chain R and 5zwo\")\n", " cmd.do(\"color grey50, chain n and 5zwo\")\n", " #PRP9\n", " cmd.do(\"color grey50, chain u and \" + object_name)\n", " cmd.do(\"color grey50, PRP9_B5zwo\")\n", " #PRP21\n", " cmd.do(\"color grey50, chain w and \" + object_name)\n", " cmd.do(\"color grey50, PRP21_B5zwo\")\n", " #SNU23\n", " cmd.do(\"color grey50, chain W and \" + object_name)\n", " cmd.do(\"color grey50, SNU23_B5zwo\")\n", " #PRP38\n", " cmd.do(\"color grey50, chain 0 and \" + object_name)\n", " cmd.do(\"color grey50, PRP38_B5zwo\")\n", " #SPP381\n", " cmd.do(\"color grey50, chain 9 and \" + object_name)\n", " cmd.do(\"color grey50, SPP381_B5zwo\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '5gm6' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '5gm6' in name.lower():\n", " #PRP8\n", " cmd.do(\"color skyblue, chain A and \" + object_name)\n", " cmd.do(\"color skyblue, PRP8_Ba5gm6\")\n", " #BRR2\n", " cmd.do(\"color grey60, chain B and \" + object_name)\n", " cmd.do(\"color grey60, BRR2_Ba5gm6\")\n", " #BUD31\n", " cmd.do(\"color dirtyviolet, chain T and \" + object_name)\n", " cmd.do(\"color dirtyviolet, BUD31_Ba5gm6\")\n", " #CEF1\n", " cmd.do(\"color raspberry, chain c and \" + object_name)\n", " cmd.do(\"color raspberry, CEF1_Ba5gm6\")\n", " #CWC15\n", " cmd.do(\"color orange, chain S and \" + object_name)\n", " cmd.do(\"color orange, CWC15_Ba5gm6\")\n", " #CWC2_hRBM22\n", " cmd.do(\"color ruby, chain R and \" + object_name)\n", " cmd.do(\"color ruby, CWC2_hRBM22_Ba5gm6\")\n", " #CWC21\n", " cmd.do(\"color violetpurple, chain X and \" + object_name)\n", " cmd.do(\"color violetpurple, CWC21_Ba5gm6\")\n", " #CWC22\n", " cmd.do(\"color bluewhite, chain Z and \" + object_name)\n", " cmd.do(\"color bluewhite, CWC22_Ba5gm6\")\n", " #PRP45\n", " cmd.do(\"color lightpink, chain P and \" + object_name)\n", " cmd.do(\"color lightpink, PRP45_Ba5gm6\")\n", " #CDC40\n", " cmd.do(\"color dirtyviolet, chain n and \" + object_name)\n", " cmd.do(\"color dirtyviolet, CDC40_Ba5gm6\")\n", " #PRP19\n", " cmd.do(\"color grey70, chain f and \" + object_name)\n", " cmd.do(\"color grey70, PRP19_Ba5gm6\")\n", " #PRP46\n", " cmd.do(\"color lightblue, chain O and \" + object_name)\n", " cmd.do(\"color lightblue, PRP46_Ba5gm6\")\n", " #SLT11/ECM2\n", " cmd.do(\"color chocolate, chain Q and \" + object_name)\n", " cmd.do(\"color chocolate, SLT11/ECM2_Ba5gm6\")\n", " #SNT309\n", " cmd.do(\"color grey70, chain t and \" + object_name)\n", " cmd.do(\"color grey70, SNT309_Ba5gm6\")\n", " #SNU114\n", " cmd.do(\"color slate, chain C and \" + object_name)\n", " cmd.do(\"color slate, SNU114_Ba5gm6\")\n", " #SYF2\n", " cmd.do(\"color brightorange, chain f and \" + object_name)\n", " cmd.do(\"color brightorange, SYF2_Ba5gm6\")\n", " #SYF1\n", " cmd.do(\"color brightorange, chain v and \" + object_name)\n", " cmd.do(\"color brightorange, SYF1_Ba5gm6\")\n", " #U2\n", " cmd.do(\"color forest, chain 2 and \" + object_name)\n", " cmd.do(\"color forest, U2_Ba5gm6\")\n", " #U5\n", " cmd.do(\"color density, chain 5 and \" + object_name)\n", " cmd.do(\"color density, U5_Ba5gm6\")\n", " #U6\n", " cmd.do(\"color firebrick, chain 6 and \" + object_name)\n", " cmd.do(\"color firebrick, U6_Ba5gm6\")\n", " #Intron\n", " cmd.do(\"color black, chain M and \" + object_name)\n", " cmd.do(\"color black, Intron_Ba5gm6\")\n", " #Exon\n", " cmd.do(\"color yellow, chain N and \" + object_name)\n", " cmd.do(\"color yellow, Exon_Ba5gm6\")\n", " #BUD13\n", " cmd.do(\"color grey60, chain W and \" + object_name)\n", " cmd.do(\"color grey60, BUD13_Ba5gm6\")\n", " #CLF2\n", " cmd.do(\"color rasberry, chain d and \" + object_name)\n", " cmd.do(\"color rasberry, CLF2_Ba5gm6\")\n", " #Cus1\n", " cmd.do(\"color palegreen, chain H and \" + object_name)\n", " cmd.do(\"color palegreen, Cus1_Ba5gm6\")\n", " #CWC24\n", " cmd.do(\"color grey60, chain a and \" + object_name)\n", " cmd.do(\"color grey60, CWC24_Ba5gm6\")\n", " #CWC27\n", " cmd.do(\"color grey60, chain b and \" + object_name)\n", " cmd.do(\"color grey60, CWC27_Ba5gm6\")\n", " #HSH155\n", " cmd.do(\"color smudge, chain G and \" + object_name)\n", " cmd.do(\"color smudge, HSH155_Ba5gm6\")\n", " #HSH49\n", " cmd.do(\"color sand, chain e and \" + object_name)\n", " cmd.do(\"color sand, HSH49_Ba5gm6\")\n", " #PML1\n", " cmd.do(\"color grey60, chain U and \" + object_name)\n", " cmd.do(\"color grey60, PML1_Ba5gm6\")\n", " #PRP11\n", " cmd.do(\"color palegreen, chain I and \" + object_name)\n", " cmd.do(\"color palegreen, PRP11_Ba5gm6\")\n", " #PRP2\n", " cmd.do(\"color palegreen, chain Y and \" + object_name)\n", " cmd.do(\"color palegreen, PRP2_Ba5gm6\")\n", " #RDS3\n", " cmd.do(\"color palegreen, chain J and \" + object_name)\n", " cmd.do(\"color palegreen, RDS3_Ba5gm6\")\n", " #RSE1\n", " cmd.do(\"color smudge, chain F and \" + object_name)\n", " cmd.do(\"color smudge, RSE1_Ba5gm6\")\n", " #SNU17\n", " cmd.do(\"color grey60, chain V and \" + object_name)\n", " cmd.do(\"color grey60, SNU17_Ba5gm6\")\n", " #Ysf3\n", " cmd.do(\"color palegreen, chain K and \" + object_name)\n", " cmd.do(\"color palegreen, Ysf3_Ba5gm6\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '5lj3' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '5lj3' in name.lower():\n", " #PRP8\n", " cmd.do(\"color skyblue, chain A and \" + object_name)\n", " cmd.do(\"color skyblue, PRP8_C5lj3\")\n", " #BUD31\n", " cmd.do(\"color dirtyviolet, chain L and \" + object_name)\n", " cmd.do(\"color dirtyviolet, BUD31_C5lj3\")\n", " #CEF1\n", " cmd.do(\"color raspberry, chain O and \" + object_name)\n", " cmd.do(\"color raspberry, CEF1_C5lj3\")\n", " #CLF1\n", " cmd.do(\"color raspberry, chain S and \" + object_name)\n", " cmd.do(\"color raspberry, CLF1_C5lj3\")\n", " #CWC15\n", " cmd.do(\"color orange, chain P and \" + object_name)\n", " cmd.do(\"color orange, CWC15_C5lj3\")\n", " #CWC16/YJU2\n", " cmd.do(\"color lightteal, chain D and \" + object_name)\n", " cmd.do(\"color lightteal, CWC16/YJU2_C5lj3\")\n", " #CWC2_hRBM22\n", " cmd.do(\"color ruby, chain M and \" + object_name)\n", " cmd.do(\"color ruby, CWC2_hRBM22_C5lj3\")\n", " #CWC21\n", " cmd.do(\"color violetpurple, chain R and \" + object_name)\n", " cmd.do(\"color violetpurple, CWC21_C5lj3\")\n", " #CWC22\n", " cmd.do(\"color bluewhite, chain H and \" + object_name)\n", " cmd.do(\"color bluewhite, CWC22_C5lj3\")\n", " #CWC25\n", " cmd.do(\"color deepteal, chain F and \" + object_name)\n", " cmd.do(\"color deepteal, CWC25_C5lj3\")\n", " #ISY1\n", " cmd.do(\"color dirtyviolet, chain G and \" + object_name)\n", " cmd.do(\"color dirtyviolet, ISY1_C5lj3\")\n", " #LEA1\n", " cmd.do(\"color palegreen, chain W and \" + object_name)\n", " cmd.do(\"color palegreen, LEA1_C5lj3\")\n", " #Msl1\n", " cmd.do(\"color palegreen, chain Y and \" + object_name)\n", " cmd.do(\"color palegreen, Msl1_C5lj3\")\n", " #PRP45\n", " cmd.do(\"color lightpink, chain K and \" + object_name)\n", " cmd.do(\"color lightpink, PRP45_C5lj3\")\n", " #PRP46\n", " cmd.do(\"color lightblue, chain J and \" + object_name)\n", " cmd.do(\"color lightblue, PRP46_C5lj3\")\n", " #SLT11/ECM2\n", " cmd.do(\"color chocolate, chain N and \" + object_name)\n", " cmd.do(\"color chocolate, SLT11/ECM2_C5lj3\")\n", " #SNU114\n", " cmd.do(\"color slate, chain C and \" + object_name)\n", " cmd.do(\"color slate, SNU114_C5lj3\")\n", " #SYF1\n", " cmd.do(\"color brightorange, chain T and \" + object_name)\n", " cmd.do(\"color brightorange, SYF1_C5lj3\")\n", " #U2\n", " cmd.do(\"color forest, chain Z and \" + object_name)\n", " cmd.do(\"color forest, U2_C5lj3\")\n", " #U5\n", " cmd.do(\"color density, chain U and \" + object_name)\n", " cmd.do(\"color density, U5_C5lj3\")\n", " #U6\n", " cmd.do(\"color firebrick, chain V and \" + object_name)\n", " cmd.do(\"color firebrick, U6_C5lj3\")\n", " #Intron\n", " cmd.do(\"color black, chain I and \" + object_name)\n", " cmd.do(\"color black, Intron_C5lj3\")\n", " #Exon\n", " cmd.do(\"color yellow, chain E and \" + object_name)\n", " cmd.do(\"color yellow, Exon_C5lj3\")\n", " cmd.do(\"color grey50, chain b and 5lj3\")\n", " cmd.do(\"color grey50, chain k and 5lj3\")\n", " cmd.do(\"color grey50, chain e and 5lj3\")\n", " cmd.do(\"color grey50, chain p and 5lj3\")\n", " cmd.do(\"color grey50, chain f and 5lj3\")\n", " cmd.do(\"color grey50, chain q and 5lj3\")\n", " cmd.do(\"color grey50, chain g and 5lj3\")\n", " cmd.do(\"color grey50, chain r and 5lj3\")\n", " cmd.do(\"color grey50, chain d and 5lj3\")\n", " cmd.do(\"color grey50, chain n and 5lj3\")\n", " cmd.do(\"color grey50, chain h and 5lj3\")\n", " cmd.do(\"color grey50, chain l and 5lj3\")\n", " cmd.do(\"color grey50, chain j and 5lj3\")\n", " cmd.do(\"color grey50, chain m and 5lj3\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '5mps' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '5mps' in name.lower():\n", " #PRP8\n", " cmd.do(\"color skyblue, chain A and \" + object_name)\n", " cmd.do(\"color skyblue, PRP8_Cs5mps\")\n", " #BUD31\n", " cmd.do(\"color dirtyviolet, chain L and \" + object_name)\n", " cmd.do(\"color dirtyviolet, BUD31_Cs5mps\")\n", " #CEF1\n", " cmd.do(\"color raspberry, chain O and \" + object_name)\n", " cmd.do(\"color raspberry, CEF1_Cs5mps\")\n", " #CLF1\n", " cmd.do(\"color raspberry, chain S and \" + object_name)\n", " cmd.do(\"color raspberry, CLF1_Cs5mps\")\n", " #CWC15\n", " cmd.do(\"color orange, chain P and \" + object_name)\n", " cmd.do(\"color orange, CWC15_Cs5mps\")\n", " #CWC2_hRBM22\n", " cmd.do(\"color ruby, chain M and \" + object_name)\n", " cmd.do(\"color ruby, CWC2_hRBM22_Cs5mps\")\n", " #CWC21\n", " cmd.do(\"color violetpurple, chain R and \" + object_name)\n", " cmd.do(\"color violetpurple, CWC21_Cs5mps\")\n", " #CWC22\n", " cmd.do(\"color bluewhite, chain H and \" + object_name)\n", " cmd.do(\"color bluewhite, CWC22_Cs5mps\")\n", " #PRP45\n", " cmd.do(\"color lightpink, chain K and \" + object_name)\n", " cmd.do(\"color lightpink, PRP45_Cs5mps\")\n", " #CDC40\n", " cmd.do(\"color dirtyviolet, chain o and \" + object_name)\n", " cmd.do(\"color dirtyviolet, CDC40_Cs5mps\")\n", " #PRP46\n", " cmd.do(\"color lightblue, chain J and \" + object_name)\n", " cmd.do(\"color lightblue, PRP46_Cs5mps\")\n", " #SLT11/ECM2\n", " cmd.do(\"color chocolate, chain N and \" + object_name)\n", " cmd.do(\"color chocolate, SLT11/ECM2_Cs5mps\")\n", " #SNU114\n", " cmd.do(\"color slate, chain C and \" + object_name)\n", " cmd.do(\"color slate, SNU114_Cs5mps\")\n", " #SYF2\n", " cmd.do(\"color brightorange, chain y and \" + object_name)\n", " cmd.do(\"color brightorange, SYF2_Cs5mps\")\n", " #SYF1\n", " cmd.do(\"color brightorange, chain T and \" + object_name)\n", " cmd.do(\"color brightorange, SYF1_Cs5mps\")\n", " #U2\n", " cmd.do(\"color forest, chain 2 and \" + object_name)\n", " cmd.do(\"color forest, U2_Cs5mps\")\n", " #U5\n", " cmd.do(\"color density, chain 5 and \" + object_name)\n", " cmd.do(\"color density, U5_Cs5mps\")\n", " #U6\n", " cmd.do(\"color firebrick, chain 6 and \" + object_name)\n", " cmd.do(\"color firebrick, U6_Cs5mps\")\n", " #5EXON\n", " cmd.do(\"color grey50, chain E and \" + object_name)\n", " cmd.do(\"color grey50, 5EXON_Cs5mps\")\n", " #Intron\n", " cmd.do(\"color black, chain I and \" + object_name)\n", " cmd.do(\"color black, Intron_Cs5mps\")\n", " #Exon\n", " cmd.do(\"color yellow, chain E and \" + object_name)\n", " cmd.do(\"color yellow, Exon_Cs5mps\")\n", " #SMB1\n", " cmd.do(\"color grey50, chain b and \" + object_name)\n", " cmd.do(\"color grey50, SMB1_Cs5mps\")\n", " #SME1\n", " cmd.do(\"color grey50, chain e and \" + object_name)\n", " cmd.do(\"color grey50, SME1_Cs5mps\")\n", " #SMX3\n", " cmd.do(\"color grey50, chain f and \" + object_name)\n", " cmd.do(\"color grey50, SMX3_Cs5mps\")\n", " #SMX2\n", " cmd.do(\"color grey50, chain g and \" + object_name)\n", " cmd.do(\"color grey50, SMX2_Cs5mps\")\n", " #SMD3\n", " cmd.do(\"color grey50, chain d and \" + object_name)\n", " cmd.do(\"color grey50, SMD3_Cs5mps\")\n", " #SMD1\n", " cmd.do(\"color grey50, chain h and \" + object_name)\n", " cmd.do(\"color grey50, SMD1_Cs5mps\")\n", " #SMD2\n", " cmd.do(\"color grey50, chain j and \" + object_name)\n", " cmd.do(\"color grey50, SMD2_Cs5mps\")\n", " #PRP18\n", " cmd.do(\"color grey50, chain a and \" + object_name)\n", " cmd.do(\"color grey50, PRP18_Cs5mps\")\n", " #SLU7\n", " cmd.do(\"color grey50, chain c and \" + object_name)\n", " cmd.do(\"color grey50, SLU7_Cs5mps\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '6exn' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '6exn' in name.lower():\n", " #PRP8\n", " cmd.do(\"color skyblue, chain A and \" + object_name)\n", " cmd.do(\"color skyblue, PRP8_P6exn\")\n", " #BUD31\n", " cmd.do(\"color dirtyviolet, chain L and \" + object_name)\n", " cmd.do(\"color dirtyviolet, BUD31_P6exn\")\n", " #CEF1\n", " cmd.do(\"color raspberry, chain O and \" + object_name)\n", " cmd.do(\"color raspberry, CEF1_P6exn\")\n", " #CLF1\n", " cmd.do(\"color raspberry, chain S and \" + object_name)\n", " cmd.do(\"color raspberry, CLF1_P6exn\")\n", " #CWC15\n", " cmd.do(\"color orange, chain P and \" + object_name)\n", " cmd.do(\"color orange, CWC15_P6exn\")\n", " #CWC16/YJU2\n", " cmd.do(\"color lightteal, chain D and \" + object_name)\n", " cmd.do(\"color lightteal, CWC16/YJU2_P6exn\")\n", " #CWC2_hRBM22\n", " cmd.do(\"color ruby, chain M and \" + object_name)\n", " cmd.do(\"color ruby, CWC2_hRBM22_P6exn\")\n", " #CWC21\n", " cmd.do(\"color violetpurple, chain R and \" + object_name)\n", " cmd.do(\"color violetpurple, CWC21_P6exn\")\n", " #CWC22\n", " cmd.do(\"color bluewhite, chain H and \" + object_name)\n", " cmd.do(\"color bluewhite, CWC22_P6exn\")\n", " #LEA1\n", " cmd.do(\"color palegreen, chain W and \" + object_name)\n", " cmd.do(\"color palegreen, LEA1_P6exn\")\n", " #Msl1\n", " cmd.do(\"color palegreen, chain Y and \" + object_name)\n", " cmd.do(\"color palegreen, Msl1_P6exn\")\n", " #PRP45\n", " cmd.do(\"color lightpink, chain K and \" + object_name)\n", " cmd.do(\"color lightpink, PRP45_P6exn\")\n", " #CDC40\n", " cmd.do(\"color dirtyviolet, chain o and \" + object_name)\n", " cmd.do(\"color dirtyviolet, CDC40_P6exn\")\n", " cmd.do(\"color grey70, chain t and 6exn\")\n", " cmd.do(\"color grey70, chain u and 6exn\")\n", " cmd.do(\"color grey70, chain v and 6exn\")\n", " cmd.do(\"color grey70, chain w and 6exn\")\n", " #PRP46\n", " cmd.do(\"color lightblue, chain J and \" + object_name)\n", " cmd.do(\"color lightblue, PRP46_P6exn\")\n", " #SLT11/ECM2\n", " cmd.do(\"color chocolate, chain N and \" + object_name)\n", " cmd.do(\"color chocolate, SLT11/ECM2_P6exn\")\n", " #SNU114\n", " cmd.do(\"color slate, chain C and \" + object_name)\n", " cmd.do(\"color slate, SNU114_P6exn\")\n", " #SYF1\n", " cmd.do(\"color brightorange, chain T and \" + object_name)\n", " cmd.do(\"color brightorange, SYF1_P6exn\")\n", " #U2\n", " cmd.do(\"color forest, chain 2 and \" + object_name)\n", " cmd.do(\"color forest, U2_P6exn\")\n", " #U5\n", " cmd.do(\"color density, chain 5 and \" + object_name)\n", " cmd.do(\"color density, U5_P6exn\")\n", " #U6\n", " cmd.do(\"color firebrick, chain 6 and \" + object_name)\n", " cmd.do(\"color firebrick, U6_P6exn\")\n", " #Intron\n", " cmd.do(\"color black, chain I and \" + object_name)\n", " cmd.do(\"color black, Intron_P6exn\")\n", " #Exon\n", " cmd.do(\"color yellow, chain E and \" + object_name)\n", " cmd.do(\"color yellow, Exon_P6exn\")\n", " cmd.do(\"color grey50, chain b and 6exn\")\n", " cmd.do(\"color grey50, chain k and 6exn\")\n", " cmd.do(\"color grey50, chain e and 6exn\")\n", " cmd.do(\"color grey50, chain p and 6exn\")\n", " cmd.do(\"color grey50, chain f and 6exn\")\n", " cmd.do(\"color grey50, chain q and 6exn\")\n", " cmd.do(\"color grey50, chain g and 6exn\")\n", " cmd.do(\"color grey50, chain r and 6exn\")\n", " cmd.do(\"color grey50, chain d and 6exn\")\n", " cmd.do(\"color grey50, chain n and 6exn\")\n", " cmd.do(\"color grey50, chain h and 6exn\")\n", " cmd.do(\"color grey50, chain l and 6exn\")\n", " cmd.do(\"color grey50, chain j and 6exn\")\n", " cmd.do(\"color grey50, chain m and 6exn\")\n", " #PRP22\n", " cmd.do(\"color grey50, chain V and \" + object_name)\n", " cmd.do(\"color grey50, PRP22_P6exn\")\n", " #PRP18\n", " cmd.do(\"color grey50, chain a and \" + object_name)\n", " cmd.do(\"color grey50, PRP18_P6exn\")\n", " #SLU7\n", " cmd.do(\"color grey50, chain c and \" + object_name)\n", " cmd.do(\"color grey50, SLU7_P6exn\")\n", " #unassigned\n", " cmd.do(\"color grey50, chain X and \" + object_name)\n", " cmd.do(\"color grey50, unassigned_P6exn\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '5ylz' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '5ylz' in name.lower():\n", " #PRP8\n", " cmd.do(\"color skyblue, chain A and \" + object_name)\n", " cmd.do(\"color skyblue, PRP8_P5ylz\")\n", " #BUD31\n", " cmd.do(\"color dirtyviolet, chain L and \" + object_name)\n", " cmd.do(\"color dirtyviolet, BUD31_P5ylz\")\n", " #CEF1\n", " cmd.do(\"color raspberry, chain J and \" + object_name)\n", " cmd.do(\"color raspberry, CEF1_P5ylz\")\n", " #CLF1\n", " cmd.do(\"color raspberry, chain I and \" + object_name)\n", " cmd.do(\"color raspberry, CLF1_P5ylz\")\n", " #CWC15\n", " cmd.do(\"color orange, chain P and \" + object_name)\n", " cmd.do(\"color orange, CWC15_P5ylz\")\n", " #CWC2_hRBM22\n", " cmd.do(\"color ruby, chain N and \" + object_name)\n", " cmd.do(\"color ruby, CWC2_hRBM22_P5ylz\")\n", " #CWC21\n", " cmd.do(\"color violetpurple, chain R and \" + object_name)\n", " cmd.do(\"color violetpurple, CWC21_P5ylz\")\n", " #CWC22\n", " cmd.do(\"color bluewhite, chain S and \" + object_name)\n", " cmd.do(\"color bluewhite, CWC22_P5ylz\")\n", " #LEA1\n", " cmd.do(\"color palegreen, chain o and \" + object_name)\n", " cmd.do(\"color palegreen, LEA1_P5ylz\")\n", " #Msl1\n", " cmd.do(\"color palegreen, chain p and \" + object_name)\n", " cmd.do(\"color palegreen, Msl1_P5ylz\")\n", " #PRP45\n", " cmd.do(\"color lightpink, chain Q and \" + object_name)\n", " cmd.do(\"color lightpink, PRP45_P5ylz\")\n", " #CDC40\n", " cmd.do(\"color dirtyviolet, chain T and \" + object_name)\n", " cmd.do(\"color dirtyviolet, CDC40_P5ylz\")\n", " cmd.do(\"color grey70, chain q and 5ylz\")\n", " cmd.do(\"color grey70, chain r and 5ylz\")\n", " cmd.do(\"color grey70, chain s and 5ylz\")\n", " cmd.do(\"color grey70, chain t and 5ylz\")\n", " #PRP46\n", " cmd.do(\"color lightblue, chain O and \" + object_name)\n", " cmd.do(\"color lightblue, PRP46_P5ylz\")\n", " #SLT11/ECM2\n", " cmd.do(\"color chocolate, chain M and \" + object_name)\n", " cmd.do(\"color chocolate, SLT11/ECM2_P5ylz\")\n", " #SNT309\n", " cmd.do(\"color grey70, chain G and \" + object_name)\n", " cmd.do(\"color grey70, SNT309_P5ylz\")\n", " #SNU114\n", " cmd.do(\"color slate, chain C and \" + object_name)\n", " cmd.do(\"color slate, SNU114_P5ylz\")\n", " #SYF2\n", " cmd.do(\"color brightorange, chain K and \" + object_name)\n", " cmd.do(\"color brightorange, SYF2_P5ylz\")\n", " #SYF1\n", " cmd.do(\"color brightorange, chain H and \" + object_name)\n", " cmd.do(\"color brightorange, SYF1_P5ylz\")\n", " #U2\n", " cmd.do(\"color forest, chain F and \" + object_name)\n", " cmd.do(\"color forest, U2_P5ylz\")\n", " #U5\n", " cmd.do(\"color density, chain B and \" + object_name)\n", " cmd.do(\"color density, U5_P5ylz\")\n", " #U6\n", " cmd.do(\"color firebrick, chain D and \" + object_name)\n", " cmd.do(\"color firebrick, U6_P5ylz\")\n", " #Intron\n", " cmd.do(\"color black, chain E and \" + object_name)\n", " cmd.do(\"color black, Intron_P5ylz\")\n", " cmd.do(\"color grey50, chain a and 5ylz\")\n", " cmd.do(\"color grey50, chain h and 5ylz\")\n", " cmd.do(\"color grey50, chain b and 5ylz\")\n", " cmd.do(\"color grey50, chain i and 5ylz\")\n", " cmd.do(\"color grey50, chain c and 5ylz\")\n", " cmd.do(\"color grey50, chain j and 5ylz\")\n", " cmd.do(\"color grey50, chain d and 5ylz\")\n", " cmd.do(\"color grey50, chain k and 5ylz\")\n", " cmd.do(\"color grey50, chain e and 5ylz\")\n", " cmd.do(\"color grey50, chain l and 5ylz\")\n", " cmd.do(\"color grey50, chain f and 5ylz\")\n", " cmd.do(\"color grey50, chain m and 5ylz\")\n", " cmd.do(\"color grey50, chain g and 5ylz\")\n", " cmd.do(\"color grey50, chain n and 5ylz\")\n", " #PRP22\n", " cmd.do(\"color grey50, chain W and \" + object_name)\n", " cmd.do(\"color grey50, PRP22_P5ylz\")\n", " #PRP18\n", " cmd.do(\"color grey50, chain U and \" + object_name)\n", " cmd.do(\"color grey50, PRP18_P5ylz\")\n", " #SLU7\n", " cmd.do(\"color grey50, chain V and \" + object_name)\n", " cmd.do(\"color grey50, SLU7_P5ylz\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '5y88' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '5y88' in name.lower():\n", " #PRP8\n", " cmd.do(\"color skyblue, chain A and \" + object_name)\n", " cmd.do(\"color skyblue, PRP8_I5y88\")\n", " #BUD31\n", " cmd.do(\"color dirtyviolet, chain L and \" + object_name)\n", " cmd.do(\"color dirtyviolet, BUD31_I5y88\")\n", " #CLF1\n", " cmd.do(\"color raspberry, chain I and \" + object_name)\n", " cmd.do(\"color raspberry, CLF1_I5y88\")\n", " #CWC15\n", " cmd.do(\"color orange, chain P and \" + object_name)\n", " cmd.do(\"color orange, CWC15_I5y88\")\n", " #CWC16/YJU2\n", " cmd.do(\"color lightteal, chain R and \" + object_name)\n", " cmd.do(\"color lightteal, CWC16/YJU2_I5y88\")\n", " #CWC2_hRBM22\n", " cmd.do(\"color ruby, chain N and \" + object_name)\n", " cmd.do(\"color ruby, CWC2_hRBM22_I5y88\")\n", " #CWC25\n", " cmd.do(\"color deepteal, chain G and \" + object_name)\n", " cmd.do(\"color deepteal, CWC25_I5y88\")\n", " #Intron_2\n", " cmd.do(\"color black, chain E and \" + object_name)\n", " cmd.do(\"color black, Intron_2_I5y88\")\n", " #LEA1\n", " cmd.do(\"color palegreen, chain o and \" + object_name)\n", " cmd.do(\"color palegreen, LEA1_I5y88\")\n", " #Msl1\n", " cmd.do(\"color palegreen, chain p and \" + object_name)\n", " cmd.do(\"color palegreen, Msl1_I5y88\")\n", " #PRP45\n", " cmd.do(\"color lightpink, chain Q and \" + object_name)\n", " cmd.do(\"color lightpink, PRP45_I5y88\")\n", " #CDC40\n", " cmd.do(\"color dirtyviolet, chain S and \" + object_name)\n", " cmd.do(\"color dirtyviolet, CDC40_I5y88\")\n", " cmd.do(\"color grey70, chain q and 5y88\")\n", " cmd.do(\"color grey70, chain r and 5y88\")\n", " cmd.do(\"color grey70, chain s and 5y88\")\n", " cmd.do(\"color grey70, chain t and 5y88\")\n", " #PRP46\n", " cmd.do(\"color lightblue, chain O and \" + object_name)\n", " cmd.do(\"color lightblue, PRP46_I5y88\")\n", " #SLT11/ECM2\n", " cmd.do(\"color chocolate, chain M and \" + object_name)\n", " cmd.do(\"color chocolate, SLT11/ECM2_I5y88\")\n", " #SNT309\n", " cmd.do(\"color grey70, chain G and \" + object_name)\n", " cmd.do(\"color grey70, SNT309_I5y88\")\n", " #SNU114\n", " cmd.do(\"color slate, chain C and \" + object_name)\n", " cmd.do(\"color slate, SNU114_I5y88\")\n", " #SYF2\n", " cmd.do(\"color brightorange, chain K and \" + object_name)\n", " cmd.do(\"color brightorange, SYF2_I5y88\")\n", " #SYF1\n", " cmd.do(\"color brightorange, chain H and \" + object_name)\n", " cmd.do(\"color brightorange, SYF1_I5y88\")\n", " #U2\n", " cmd.do(\"color forest, chain F and \" + object_name)\n", " cmd.do(\"color forest, U2_I5y88\")\n", " #U5\n", " cmd.do(\"color density, chain B and \" + object_name)\n", " cmd.do(\"color density, U5_I5y88\")\n", " #U6\n", " cmd.do(\"color firebrick, chain D and \" + object_name)\n", " cmd.do(\"color firebrick, U6_I5y88\")\n", " #Intron\n", " cmd.do(\"color black, chain x and \" + object_name)\n", " cmd.do(\"color black, Intron_I5y88\")\n", " #RNA\n", " cmd.do(\"color grey50, chain x and \" + object_name)\n", " cmd.do(\"color grey50, RNA_I5y88\")\n", " #cwc23\n", " cmd.do(\"color grey50, chain T and \" + object_name)\n", " cmd.do(\"color grey50, cwc23_I5y88\")\n", " #SPP382\n", " cmd.do(\"color grey50, chain U and \" + object_name)\n", " cmd.do(\"color grey50, SPP382_I5y88\")\n", " #NTR2\n", " cmd.do(\"color grey50, chain V and \" + object_name)\n", " cmd.do(\"color grey50, NTR2_I5y88\")\n", " #PRP43\n", " cmd.do(\"color grey50, chain W and \" + object_name)\n", " cmd.do(\"color grey50, PRP43_I5y88\")\n", " cmd.do(\"color grey50, chain a and 5y88\")\n", " cmd.do(\"color grey50, chain h and 5y88\")\n", " cmd.do(\"color grey50, chain b and 5y88\")\n", " cmd.do(\"color grey50, chain i and 5y88\")\n", " cmd.do(\"color grey50, chain c and 5y88\")\n", " cmd.do(\"color grey50, chain j and 5y88\")\n", " cmd.do(\"color grey50, chain d and 5y88\")\n", " cmd.do(\"color grey50, chain k and 5y88\")\n", " cmd.do(\"color grey50, chain e and 5y88\")\n", " cmd.do(\"color grey50, chain l and 5y88\")\n", " cmd.do(\"color grey50, chain f and 5y88\")\n", " cmd.do(\"color grey50, chain m and 5y88\")\n", " cmd.do(\"color grey50, chain g and 5y88\")\n", " cmd.do(\"color grey50, chain n and 5y88\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '3jb9' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '3jb9' in name.lower():\n", " #U2\n", " cmd.do(\"color forest, chain P and \" + object_name)\n", " cmd.do(\"color forest, U2_3jb9\")\n", " #U5\n", " cmd.do(\"color density, chain C and \" + object_name)\n", " cmd.do(\"color density, U5_3jb9\")\n", " #U6\n", " cmd.do(\"color firebrick, chain N and \" + object_name)\n", " cmd.do(\"color firebrick, U6_3jb9\")\n", " cmd.do(\"color black, chain O and 3jb9\")\n", " cmd.do(\"color black, chain Q and 3jb9\")\n", " #Spp42_yPrp8\n", " cmd.do(\"color grey50, chain A and \" + object_name)\n", " cmd.do(\"color grey50, Spp42_yPrp8_3jb9\")\n", " #CWF15_yCWC15\n", " cmd.do(\"color orange, chain h and \" + object_name)\n", " cmd.do(\"color orange, CWF15_yCWC15_3jb9\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '6icz' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '6icz' in name.lower():\n", " #CWC15\n", " cmd.do(\"color orange, chain P and \" + object_name)\n", " cmd.do(\"color orange, CWC15_hP_6icz\")\n", " #U2\n", " cmd.do(\"color forest, chain H and \" + object_name)\n", " cmd.do(\"color forest, U2_hP_6icz\")\n", " #U5\n", " cmd.do(\"color density, chain B and \" + object_name)\n", " cmd.do(\"color density, U5_hP_6icz\")\n", " #U6\n", " cmd.do(\"color firebrick, chain F and \" + object_name)\n", " cmd.do(\"color firebrick, U6_hP_6icz\")\n", " #Intron\n", " cmd.do(\"color black, chain G and \" + object_name)\n", " cmd.do(\"color black, Intron_hP_6icz\")\n", " #cwc23\n", " cmd.do(\"color grey50, chain 6ICZ and \" + object_name)\n", " cmd.do(\"color grey50, cwc23_hP_6icz\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '6ff7' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '6ff7' in name.lower():\n", " #CWC15\n", " cmd.do(\"color orange, chain R and \" + object_name)\n", " cmd.do(\"color orange, CWC15_hBa_6ff7\")\n", " #CWC2_hRBM22\n", " cmd.do(\"color ruby, chain P and \" + object_name)\n", " cmd.do(\"color ruby, CWC2_hRBM22_hBa_6ff7\")\n", " #U2\n", " cmd.do(\"color forest, chain 2 and \" + object_name)\n", " cmd.do(\"color forest, U2_hBa_6ff7\")\n", " #U5\n", " cmd.do(\"color density, chain 5 and \" + object_name)\n", " cmd.do(\"color density, U5_hBa_6ff7\")\n", " #U6\n", " cmd.do(\"color firebrick, chain 6 and \" + object_name)\n", " cmd.do(\"color firebrick, U6_hBa_6ff7\")\n", " #Intron\n", " cmd.do(\"color black, chain Z and \" + object_name)\n", " cmd.do(\"color black, Intron_hBa_6ff7\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '5yzg' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '5yzg' in name.lower():\n", " #CWC15\n", " cmd.do(\"color orange, chain P and \" + object_name)\n", " cmd.do(\"color orange, CWC15_hC_5yzg\")\n", " #CWC2_hRBM22\n", " cmd.do(\"color ruby, chain O and \" + object_name)\n", " cmd.do(\"color ruby, CWC2_hRBM22_hC_5yzg\")\n", " #CWC25\n", " cmd.do(\"color deepteal, chain X and \" + object_name)\n", " cmd.do(\"color deepteal, CWC25_hC_5yzg\")\n", " #PRP16_hDHX38\n", " cmd.do(\"color smudge, chain Z and \" + object_name)\n", " cmd.do(\"color smudge, PRP16_hDHX38_hC_5yzg\")\n", " #U2\n", " cmd.do(\"color forest, chain H and \" + object_name)\n", " cmd.do(\"color forest, U2_hC_5yzg\")\n", " #U5\n", " cmd.do(\"color density, chain B and \" + object_name)\n", " cmd.do(\"color density, U5_hC_5yzg\")\n", " #U6\n", " cmd.do(\"color firebrick, chain F and \" + object_name)\n", " cmd.do(\"color firebrick, U6_hC_5yzg\")\n", " #Intron\n", " cmd.do(\"color black, chain G and \" + object_name)\n", " cmd.do(\"color black, Intron_hC_5yzg\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '5xjc' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '5xjc' in name.lower():\n", " #CWC15\n", " cmd.do(\"color orange, chain P and \" + object_name)\n", " cmd.do(\"color orange, CWC15_hX_5xjc\")\n", " #CWC25\n", " cmd.do(\"color deepteal, chain X and \" + object_name)\n", " cmd.do(\"color deepteal, CWC25_hX_5xjc\")\n", " #U2\n", " cmd.do(\"color forest, chain H and \" + object_name)\n", " cmd.do(\"color forest, U2_hX_5xjc\")\n", " #U5\n", " cmd.do(\"color density, chain B and \" + object_name)\n", " cmd.do(\"color density, U5_hX_5xjc\")\n", " #U6\n", " cmd.do(\"color firebrick, chain F and \" + object_name)\n", " cmd.do(\"color firebrick, U6_hX_5xjc\")\n", " #Intron\n", " cmd.do(\"color black, chain G and \" + object_name)\n", " cmd.do(\"color black, Intron_hX_5xjc\")\n", " #PRKRIP1\n", " cmd.do(\"color grey50, chain X and \" + object_name)\n", " cmd.do(\"color grey50, PRKRIP1_hX_5xjc\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '5gan' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '5gan' in name.lower():\n", " #PRP8\n", " cmd.do(\"color skyblue, chain A and \" + object_name)\n", " cmd.do(\"color skyblue, PRP8_y3_5gan\")\n", " #BRR2\n", " cmd.do(\"color grey60, chain B and \" + object_name)\n", " cmd.do(\"color grey60, BRR2_y3_5gan\")\n", " #PRP45\n", " cmd.do(\"color lightpink, chain H and \" + object_name)\n", " cmd.do(\"color lightpink, PRP45_y3_5gan\")\n", " #SNU114\n", " cmd.do(\"color slate, chain C and \" + object_name)\n", " cmd.do(\"color slate, SNU114_y3_5gan\")\n", " #U5\n", " cmd.do(\"color density, chain U and \" + object_name)\n", " cmd.do(\"color density, U5_y3_5gan\")\n", " #U6\n", " cmd.do(\"color firebrick, chain W and \" + object_name)\n", " cmd.do(\"color firebrick, U6_y3_5gan\")\n", " #U4\n", " cmd.do(\"color brown, chain V and \" + object_name)\n", " cmd.do(\"color brown, U4_y3_5gan\")\n", " #PRP31\n", " cmd.do(\"color grey50, chain F and \" + object_name)\n", " cmd.do(\"color grey50, PRP31_y3_5gan\")\n", " #PRP6\n", " cmd.do(\"color grey50, chain J and \" + object_name)\n", " cmd.do(\"color grey50, PRP6_y3_5gan\")\n", " #PRP3\n", " cmd.do(\"color grey50, chain G and \" + object_name)\n", " cmd.do(\"color grey50, PRP3_y3_5gan\")\n", " #DIB1\n", " cmd.do(\"color grey50, chain D and \" + object_name)\n", " cmd.do(\"color grey50, DIB1_y3_5gan\")\n", " #SNU13\n", " cmd.do(\"color grey50, chain K and \" + object_name)\n", " cmd.do(\"color grey50, SNU13_y3_5gan\")\n", " #LSM8\n", " cmd.do(\"color grey50, chain 8 and \" + object_name)\n", " cmd.do(\"color grey50, LSM8_y3_5gan\")\n", " #LSM2\n", " cmd.do(\"color grey50, chain 2 and \" + object_name)\n", " cmd.do(\"color grey50, LSM2_y3_5gan\")\n", " #LSM3\n", " cmd.do(\"color grey50, chain 3 and \" + object_name)\n", " cmd.do(\"color grey50, LSM3_y3_5gan\")\n", " #LSM6\n", " cmd.do(\"color grey50, chain 6 and \" + object_name)\n", " cmd.do(\"color grey50, LSM6_y3_5gan\")\n", " #LSM5\n", " cmd.do(\"color grey50, chain 5 and \" + object_name)\n", " cmd.do(\"color grey50, LSM5_y3_5gan\")\n", " #LSM7\n", " cmd.do(\"color grey50, chain 7 and \" + object_name)\n", " cmd.do(\"color grey50, LSM7_y3_5gan\")\n", " #LSM4\n", " cmd.do(\"color grey50, chain 4 and \" + object_name)\n", " cmd.do(\"color grey50, LSM4_y3_5gan\")\n", " #SNU66\n", " cmd.do(\"color grey50, chain E and \" + object_name)\n", " cmd.do(\"color grey50, SNU66_y3_5gan\")\n", " cmd.do(\"color grey50, chain b and 5gan\")\n", " cmd.do(\"color grey50, chain k and 5gan\")\n", " cmd.do(\"color grey50, chain e and 5gan\")\n", " cmd.do(\"color grey50, chain p and 5gan\")\n", " cmd.do(\"color grey50, chain f and 5gan\")\n", " cmd.do(\"color grey50, chain q and 5gan\")\n", " cmd.do(\"color grey50, chain g and 5gan\")\n", " cmd.do(\"color grey50, chain r and 5gan\")\n", " cmd.do(\"color grey50, chain d and 5gan\")\n", " cmd.do(\"color grey50, chain n and 5gan\")\n", " cmd.do(\"color grey50, chain h and 5gan\")\n", " cmd.do(\"color grey50, chain l and 5gan\")\n", " cmd.do(\"color grey50, chain j and 5gan\")\n", " cmd.do(\"color grey50, chain m and 5gan\")\n", " #unassigned\n", " cmd.do(\"color grey50, chain X and \" + object_name)\n", " cmd.do(\"color grey50, unassigned_y3_5gan\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '6qw6' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '6qw6' in name.lower():\n", " #PRP8\n", " cmd.do(\"color skyblue, chain 5A and \" + object_name)\n", " cmd.do(\"color skyblue, PRP8_h3_6qw6\")\n", " #U5\n", " cmd.do(\"color density, chain 5 and \" + object_name)\n", " cmd.do(\"color density, U5_h3_6qw6\")\n", " #U6\n", " cmd.do(\"color firebrick, chain 6 and \" + object_name)\n", " cmd.do(\"color firebrick, U6_h3_6qw6\")\n", " #U4\n", " cmd.do(\"color brown, chain 4 and \" + object_name)\n", " cmd.do(\"color brown, U4_h3_6qw6\")\n", " #Prp28\n", " cmd.do(\"color red, chain 5X and \" + object_name)\n", " cmd.do(\"color red, Prp28_h3_6qw6\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '3jcr' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '3jcr' in name.lower():\n", " #PRP8\n", " cmd.do(\"color skyblue, chain A and \" + object_name)\n", " cmd.do(\"color skyblue, PRP8_h3_3jcr\")\n", " #BRR2\n", " cmd.do(\"color grey60, chain C and \" + object_name)\n", " cmd.do(\"color grey60, BRR2_h3_3jcr\")\n", " #SNU114\n", " cmd.do(\"color slate, chain B and \" + object_name)\n", " cmd.do(\"color slate, SNU114_h3_3jcr\")\n", " #U5\n", " cmd.do(\"color density, chain H and \" + object_name)\n", " cmd.do(\"color density, U5_h3_3jcr\")\n", " #U6\n", " cmd.do(\"color firebrick, chain N and \" + object_name)\n", " cmd.do(\"color firebrick, U6_h3_3jcr\")\n", " #U4\n", " cmd.do(\"color brown, chain M and \" + object_name)\n", " cmd.do(\"color brown, U4_h3_3jcr\")\n", " #PRP4\n", " cmd.do(\"color grey50, chain L and \" + object_name)\n", " cmd.do(\"color grey50, PRP4_h3_3jcr\")\n", " #PRP31\n", " cmd.do(\"color grey50, chain J and \" + object_name)\n", " cmd.do(\"color grey50, PRP31_h3_3jcr\")\n", " #PRP6\n", " cmd.do(\"color grey50, chain G and \" + object_name)\n", " cmd.do(\"color grey50, PRP6_h3_3jcr\")\n", " #PRP3\n", " cmd.do(\"color grey50, chain K and \" + object_name)\n", " cmd.do(\"color grey50, PRP3_h3_3jcr\")\n", " #SNU13\n", " cmd.do(\"color grey50, chain I and \" + object_name)\n", " cmd.do(\"color grey50, SNU13_h3_3jcr\")\n", " #LSM8\n", " cmd.do(\"color grey50, chain 8 and \" + object_name)\n", " cmd.do(\"color grey50, LSM8_h3_3jcr\")\n", " #LSM2\n", " cmd.do(\"color grey50, chain 2 and \" + object_name)\n", " cmd.do(\"color grey50, LSM2_h3_3jcr\")\n", " #LSM3\n", " cmd.do(\"color grey50, chain 3 and \" + object_name)\n", " cmd.do(\"color grey50, LSM3_h3_3jcr\")\n", " #LSM5\n", " cmd.do(\"color grey50, chain 5 and \" + object_name)\n", " cmd.do(\"color grey50, LSM5_h3_3jcr\")\n", " #LSM7\n", " cmd.do(\"color grey50, chain 7 and \" + object_name)\n", " cmd.do(\"color grey50, LSM7_h3_3jcr\")\n", " #LSM4\n", " cmd.do(\"color grey50, chain 4 and \" + object_name)\n", " cmd.do(\"color grey50, LSM4_h3_3jcr\")\n", " cmd.do(\"color grey50, chain R and 3jcr\")\n", " cmd.do(\"color grey50, chain r and 3jcr\")\n", " cmd.do(\"color grey50, chain P and 3jcr\")\n", " cmd.do(\"color grey50, chain p and 3jcr\")\n", " cmd.do(\"color grey50, chain Q and 3jcr\")\n", " cmd.do(\"color grey50, chain q and 3jcr\")\n", " #U5-40K\n", " cmd.do(\"color grey71, chain D and \" + object_name)\n", " cmd.do(\"color grey71, U5-40K_h3_3jcr\")\n", " #Dim1\n", " cmd.do(\"color grey60, chain E and \" + object_name)\n", " cmd.do(\"color grey60, Dim1_h3_3jcr\")\n", " #Prp28\n", " cmd.do(\"color red, chain F and \" + object_name)\n", " cmd.do(\"color red, Prp28_h3_3jcr\")\n", " cmd.do(\"color grey60, chain S and 3jcr\")\n", " cmd.do(\"color grey60, chain s and 3jcr\")\n", " cmd.do(\"color grey60, chain T and 3jcr\")\n", " cmd.do(\"color grey60, chain t and 3jcr\")\n", " cmd.do(\"color grey60, chain U and 3jcr\")\n", " cmd.do(\"color grey60, chain u and 3jcr\")\n", " #Sad1\n", " cmd.do(\"color grey60, chain V and \" + object_name)\n", " cmd.do(\"color grey60, Sad1_h3_3jcr\")\n", " cmd.do(\"color grey60, chain O and 3jcr\")\n", " cmd.do(\"color grey60, chain o and 3jcr\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '6qx9' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '6qx9' in name.lower():\n", " #PRP8\n", " cmd.do(\"color skyblue, chain 5A and \" + object_name)\n", " cmd.do(\"color skyblue, PRP8_h3_6qx9\")\n", " #U2\n", " cmd.do(\"color forest, chain 2 and \" + object_name)\n", " cmd.do(\"color forest, U2_h3_6qx9\")\n", " #U5\n", " cmd.do(\"color density, chain 5 and \" + object_name)\n", " cmd.do(\"color density, U5_h3_6qx9\")\n", " #U6\n", " cmd.do(\"color firebrick, chain 6 and \" + object_name)\n", " cmd.do(\"color firebrick, U6_h3_6qx9\")\n", " #U4\n", " cmd.do(\"color brown, chain 4 and \" + object_name)\n", " cmd.do(\"color brown, U4_h3_6qx9\")\n", " #Intron\n", " cmd.do(\"color black, chain I and \" + object_name)\n", " cmd.do(\"color black, Intron_h3_6qx9\")\n", " #U1\n", " cmd.do(\"color green, chain 1 and \" + object_name)\n", " cmd.do(\"color green, U1_h3_6qx9\")\n", " #Prp28\n", " cmd.do(\"color red, chain 5X and \" + object_name)\n", " cmd.do(\"color red, Prp28_h3_6qx9\")\n", " \n", " for n in cmd.get_names(\"all\"):\n", " if '6ah0' in n:\n", " object_name = n\n", " print(object_name)\n", " \n", " if '6ah0' in name.lower():\n", " #PRP8\n", " cmd.do(\"color skyblue, chain A and \" + object_name)\n", " cmd.do(\"color skyblue, PRP8_h_Bp_6ah0\")\n", " #U2\n", " cmd.do(\"color forest, chain H and \" + object_name)\n", " cmd.do(\"color forest, U2_h_Bp_6ah0\")\n", " #U5\n", " cmd.do(\"color density, chain B and \" + object_name)\n", " cmd.do(\"color density, U5_h_Bp_6ah0\")\n", " #U6\n", " cmd.do(\"color firebrick, chain F and \" + object_name)\n", " cmd.do(\"color firebrick, U6_h_Bp_6ah0\")\n", " #U4\n", " cmd.do(\"color brown, chain I and \" + object_name)\n", " cmd.do(\"color brown, U4_h_Bp_6ah0\")\n", " #Intron\n", " cmd.do(\"color black, chain G and \" + object_name)\n", " cmd.do(\"color black, Intron_h_Bp_6ah0\")\n", " #Prp28\n", " cmd.do(\"color red, chain X and \" + object_name)\n", " cmd.do(\"color red, Prp28_h_Bp_6ah0\")\n", "\n" ] } ], "source": [ "txt = \"\"\"\n", "try:\n", " from pymol import cmd\n", "except ImportError:\n", " print(\"PyMOL Python lib is missing\")\n", " # sys.exit(0)\n", "\n", "def spl_color():\n", " for name in cmd.get_names(\"all\"):\n", " # cmd.do('color grey50') # off gray\n", " #if name in \"\"\" + strs + \"\"\": # this should be auto\n", " print(\" \\ Extracting mode for %s\" % name)\n", "\"\"\"\n", "\n", "for struc_col, pdb_id, complex_code in strucs:\n", " txt += \"\"\" \n", " for n in cmd.get_names(\"all\"):\n", " if '%s' in n:\n", " object_name = n\n", " print(object_name)\n", " \\n\"\"\" % pdb_id\n", " \n", " txt += \" if '\" + pdb_id + \"' in name.lower():\\n\"\n", " for index, i in df.iterrows():\n", " ref = str(i['chain']).strip()\n", " struc = str(i[struc_col]).strip()\n", " # print(ref, struc)\n", " # todo fix cmd.extract(\"CDC40 (PRP17, SLU4, XRS2)\", \"chain n\")\n", " i['protein'] = i['protein'].split()[0]\n", " if struc != 'nan' and struc != '-': # if ref != 'nan' # i dont' use reference chain any more\n", " if ',' in struc:\n", " subchains = struc.split(',') # a,P,h\n", " for index , sc in enumerate(subchains): \n", " sc = sc.strip()\n", " # cmd.extract(name, selection, source_state, target_state)\n", " txt += ' cmd.do(\"color ' + i['color'] + \\\n", " ', chain ' + sc + ' and ' + pdb_id + '\")\\n'\n", " # one mode to see these two proteins\n", " #print(' cmd.extract(\"' + i['protein'] + '\", \"chain ' + '+'.join(subchains) + '\")') \n", " else:\n", " #if ref != struc:\n", " txt += ' #' + i['protein'] +'\\n'\n", " txt += ' cmd.do(\"color ' + i['color'] + ', chain ' + struc + ' and \" + object_name)' + '\\n'\n", " # color \n", " txt += ' cmd.do(\"color ' + i['color'] + ', ' + i['protein'] + \\\n", " complex_code + '\")\\n'\n", "print(txt) \n", "\n", "with open(path + 'code_for_color_spl.py', 'w') as f:\n", " f.write(txt) " ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "hide_input": false, "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.7.4" }, "toc": { "colors": { "hover_highlight": "#DAA520", "running_highlight": "#FF0000", "selected_highlight": "#FFD700" }, "moveMenuLeft": true, "nav_menu": { "height": "12px", "width": "252px" }, "navigate_menu": true, "number_sections": true, "sideBar": true, "threshold": 4, "toc_cell": false, "toc_position": { "height": "625px", "left": "0px", "right": "814px", "top": "134px", "width": "26px" }, "toc_section_display": "block", "toc_window_display": true, "widenNotebook": false } }, "nbformat": 4, "nbformat_minor": 2 }