{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "

\"Вернуться\n", "Tikhonova Polina. Homework 6.

" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": true }, "outputs": [], "source": [ "import sys \n", "import modeller \n", "import _modeller\n", "import modeller.automodel \n", "import nglview" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", " MODELLER 9.19, 2017/07/19, r11078\n", "\n", " PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS\n", "\n", "\n", " Copyright(c) 1989-2017 Andrej Sali\n", " All Rights Reserved\n", "\n", " Written by A. Sali\n", " with help from\n", " B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,\n", " M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,\n", " A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,\n", " F. Melo, J.P. Overington, E. Feyfant\n", " University of California, San Francisco, USA\n", " Rockefeller University, New York, USA\n", " Harvard University, Cambridge, USA\n", " Imperial Cancer Research Fund, London, UK\n", " Birkbeck College, University of London, London, UK\n", "\n", "\n", "Kind, OS, HostName, Kernel, Processor: 4, Linux shadbox 3.2.0-29-generic x86_64\n", "Date and time of compilation : 2017/07/19 14:40:43\n", "MODELLER executable type : x86_64-intel8\n", "Job starting time (YY/MM/DD HH:MM:SS): 2017/12/02 23:53:11\n", "\n" ] } ], "source": [ "env=modeller.environ()\n", "env.io.hetatm=True" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Взяла белок ли́сого кузу́ (или щёткохвост, или лисовидный поссум, или обыкновенный кузу-лиса — млекопитающее семейства кускусовых).\n", "" ] }, { "cell_type": "raw", "metadata": {}, "source": [ "! wget http://www.pdb.org/pdb/files/1lmp.pdb" ] }, { "cell_type": "raw", "metadata": { "collapsed": true }, "source": [ "! wget http://www.uniprot.org/uniprot/P51782.fasta" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": true }, "outputs": [], "source": [ "alignm=modeller.alignment(env)" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "read_pd_459W> Residue type NAG not recognized. 'automodel' model building\n", " will treat this residue as a rigid body.\n", " To use real parameters, add the residue type to ${LIB}/restyp.lib,\n", " its topology to ${LIB}/top_*.lib, and suitable forcefield\n", " parameters to ${LIB}/par.lib.\n", "rdpdb___459W> Residue type NDG not recognized. 'automodel' model building\n", " will treat this residue as a rigid body.\n", " To use real parameters, add the residue type to ${LIB}/restyp.lib,\n", " its topology to ${LIB}/top_*.lib, and suitable forcefield\n", " parameters to ${LIB}/par.lib.\n" ] } ], "source": [ "alignm.append(file='P51782.fasta', align_codes='all',alignment_format='FASTA')\n", "## создадим модель\n", "mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))\n", "## и добавим в выравнивание\n", "alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')\n", "alignm[0].code = 'without_ligand'" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "SALIGN_____> adding the next group to the alignment; iteration 1\n" ] } ], "source": [ "alignm.salign()\n", "alignm.write(file='all_in_one.ali', alignment_format='PIR')\n", "alignm[0].code = 'without_ligand'" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "without_ligand 1lmp\n", "fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA\n", " (This is usually caused by non-standard residues, such\n", " as ligands, or by PDB files with missing atoms.)\n", "fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA\n", " (This is usually caused by non-standard residues, such\n", " as ligands, or by PDB files with missing atoms.)\n", "\n", "check_ali___> Checking the sequence-structure alignment. \n", "\n", "Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:\n", "\n", "ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST\n", "----------------------------------------------\n", "END OF TABLE\n", "read_to_681_> topology.submodel read from topology file: 3\n", "fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA\n", " (This is usually caused by non-standard residues, such\n", " as ligands, or by PDB files with missing atoms.)\n", "patch_s_522_> Number of disulfides patched in MODEL: 4\n", "mdtrsr__446W> A potential that relies on one protein is used, yet you have at\n", " least one known structure available. MDT, not library, potential is used.\n", "iup2crm_280W> No topology library in memory or assigning a BLK residue.\n", " Default CHARMM atom type assigned: C1 --> CT2\n", " This message is written only for the first such atom.\n", "0 atoms in HETATM/BLK residues constrained\n", "to protein atoms within 2.30 angstroms\n", "and protein CA atoms within 10.00 angstroms\n", "0 atoms in residues without defined topology\n", "constrained to be rigid bodies\n", "condens_443_> Restraints marked for deletion were removed.\n", " Total number of restraints before, now: 13014 11982\n", "\n", "\n", ">> ENERGY; Differences between the model's features and restraints:\n", "Number of all residues in MODEL : 147\n", "Number of all, selected real atoms : 1179 1179\n", "Number of all, selected pseudo atoms : 0 0\n", "Number of all static, selected restraints : 11982 11982\n", "COVALENT_CYS : F\n", "NONBONDED_SEL_ATOMS : 1\n", "Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2358\n", "Dynamic pairs routine : 2, NATM x NATM cell sorting\n", "Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390\n", "LENNARD_JONES_SWITCH : 6.500 7.500\n", "COULOMB_JONES_SWITCH : 6.500 7.500\n", "RESIDUE_SPAN_RANGE : 0 99999\n", "NLOGN_USE : 15\n", "CONTACT_SHELL : 4.000\n", "DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F\n", "SPHERE_STDV : 0.050\n", "RADII_FACTOR : 0.820\n", "Current energy : 790.6201\n", "\n", "\n", "\n", "\n", "\n", "Summary of the restraint violations: \n", "\n", " NUM ... number of restraints.\n", " NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].\n", " RVIOL ... relative difference from the best value.\n", " NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].\n", " RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).\n", " RMS_2 ... RMS(feature, best_value, NUMB).\n", " MOL.PDF ... scaled contribution to -Ln(Molecular pdf).\n", "\n", " # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i\n", "------------------------------------------------------------------------------------------------------\n", " 1 Bond length potential : 1205 0 0 0.006 0.006 12.310 1.000\n", " 2 Bond angle potential : 1624 0 5 1.969 1.969 127.56 1.000\n", " 3 Stereochemical cosine torsion poten: 773 0 36 48.801 48.801 280.90 1.000\n", " 4 Stereochemical improper torsion pot: 506 0 0 1.244 1.244 18.239 1.000\n", " 5 Soft-sphere overlap restraints : 2358 0 0 0.001 0.001 0.54846 1.000\n", " 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000\n", " 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000\n", " 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000\n", " 9 Distance restraints 1 (CA-CA) : 2380 0 3 0.146 0.146 42.705 1.000\n", "10 Distance restraints 2 (N-O) : 2535 0 0 0.183 0.183 73.640 1.000\n", "11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "13 Mainchain Omega dihedral restraints: 146 0 1 4.219 4.219 30.652 1.000\n", "14 Sidechain Chi_1 dihedral restraints: 125 0 0 61.593 61.593 8.5635 1.000\n", "15 Sidechain Chi_2 dihedral restraints: 98 0 0 75.037 75.037 37.092 1.000\n", "16 Sidechain Chi_3 dihedral restraints: 40 0 1 84.580 84.580 28.607 1.000\n", "17 Sidechain Chi_4 dihedral restraints: 19 0 0 81.349 81.349 11.549 1.000\n", "18 Disulfide distance restraints : 4 0 0 0.006 0.006 0.27971E-01 1.000\n", "19 Disulfide angle restraints : 8 0 0 1.711 1.711 0.51698 1.000\n", "20 Disulfide dihedral angle restraints: 4 0 0 28.648 28.648 3.2186 1.000\n", "21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "23 Distance restraints 3 (SDCH-MNCH) : 1577 0 0 0.395 0.395 23.522 1.000\n", "24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000\n", "25 Phi/Psi pair of dihedral restraints: 145 16 20 22.136 57.429 44.195 1.000\n", "26 Distance restraints 4 (SDCH-SDCH) : 793 0 0 0.725 0.725 46.776 1.000\n", "27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000\n", "28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000\n", "29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000\n", "30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000\n", "36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000\n", "37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000\n", "38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "\n", "\n", "\n", "# Heavy relative violation of each residue is written to: without_ligand.V99990001\n", "# The profile is NOT normalized by the number of restraints.\n", "# The profiles are smoothed over a window of residues: 1\n", "# The sum of all numbers in the file: 14269.7188\n", "\n", "\n", "\n", "List of the violated restraints:\n", " A restraint is violated when the relative difference\n", " from the best value (RVIOL) is larger than CUTOFF.\n", "\n", " ICSR ... index of a restraint in the current set.\n", " RESNO ... residue numbers of the first two atoms.\n", " ATM ... IUPAC atom names of the first two atoms.\n", " FEAT ... the value of the feature in the model.\n", " restr ... the mean of the basis restraint with the smallest\n", " difference from the model (local minimum).\n", " viol ... difference from the local minimum.\n", " rviol ... relative difference from the local minimum.\n", " RESTR ... the best value (global minimum).\n", " VIOL ... difference from the best value.\n", " RVIOL ... relative difference from the best value.\n", "\n", "\n", "-------------------------------------------------------------------------------------------------\n", "\n", "Feature 25 : Phi/Psi pair of dihedral restraints \n", "List of the RVIOL violations larger than : 6.5000\n", "\n", " # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL\n", " 1 4127 3V 4L C N 23 25 -118.82 -108.50 44.55 2.29 -63.50 153.29 24.71\n", " 1 4L 4L N CA 25 26 175.84 132.50 -41.20\n", " 2 4129 5L 6L C N 39 41 -152.04 -108.50 43.82 2.15 -63.50 -169.46 23.34\n", " 2 6L 6L N CA 41 42 127.52 132.50 -41.20\n", " 3 4130 6L 7L C N 47 49 -133.26 -108.50 28.57 1.54 -63.50 174.05 21.41\n", " 3 7L 7L N CA 49 50 118.25 132.50 -41.20\n", " 4 4131 7L 8G C N 55 57 69.34 78.70 15.64 0.79 82.20 173.34 7.76\n", " 4 8G 8G N CA 57 58 -178.63 -166.10 8.50\n", " 5 4132 8G 9F C N 59 61 -132.74 -124.20 12.89 0.36 -63.20 176.98 29.11\n", " 5 9F 9F N CA 61 62 152.95 143.30 -44.30\n", " 6 4134 10I 11F C N 78 80 -99.40 -124.20 40.70 1.19 -63.20 159.49 19.86\n", " 6 11F 11F N CA 80 81 111.03 143.30 -44.30\n", " 7 4136 12C 13S C N 95 97 -78.33 -72.40 14.05 0.66 -64.10 160.49 12.53\n", " 7 13S 13S N CA 97 98 165.14 152.40 -35.00\n", " 8 4137 13S 14M C N 101 103 -72.52 -73.00 6.59 0.45 -63.40 170.17 26.12\n", " 8 14M 14M N CA 103 104 149.57 143.00 -40.50\n", " 9 4138 14M 15A C N 109 111 -125.52 -134.00 10.68 0.59 -62.50 177.20 32.41\n", " 9 15A 15A N CA 111 112 153.49 147.00 -40.90\n", " 10 4139 15A 16A C N 114 116 -135.89 -134.00 12.49 0.66 -62.50 175.81 32.74\n", " 10 16A 16A N CA 116 117 159.34 147.00 -40.90\n", " 11 4140 16A 17H C N 119 121 -107.99 -125.60 21.78 0.97 -63.20 172.02 24.43\n", " 11 17H 17H N CA 121 122 151.62 138.80 -42.30\n", " 12 4141 17H 18G C N 129 131 128.64 78.70 52.88 2.14 82.20 174.31 10.70\n", " 12 18G 18G N CA 131 132 176.51 -166.10 8.50\n", " 13 4142 18G 19K C N 133 135 -68.65 -70.20 20.62 1.46 -62.90 160.74 20.57\n", " 13 19K 19K N CA 135 136 119.84 140.40 -40.80\n", " 14 4177 53E 54S C N 436 438 -137.47 -64.10 81.11 8.55 -64.10 81.11 8.55\n", " 14 54S 54S N CA 438 439 -0.42 -35.00 -35.00\n", " 15 4188 64N 65P C N 521 523 -73.93 -64.50 9.81 1.08 -58.70 175.66 13.32\n", " 15 65P 65P N CA 523 524 144.50 147.20 -30.50\n", " 16 4241 117I 118V C N 932 934 -61.42 -62.40 51.11 6.53 -62.40 51.11 6.53\n", " 16 118V 118V N CA 934 935 8.71 -42.40 -42.40\n", "\n", "\n", "report______> Distribution of short non-bonded contacts:\n", "\n", "\n", "DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40\n", "DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50\n", "FREQUENCY: 0 0 0 0 0 3 8 45 75 116 98 129 155 171 183\n", "\n", "\n", "<< end of ENERGY.\n", "iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.\n", "\n", "\n", ">> ENERGY; Differences between the model's features and restraints:\n", "Number of all residues in MODEL : 147\n", "Number of all, selected real atoms : 1179 1179\n", "Number of all, selected pseudo atoms : 0 0\n", "Number of all static, selected restraints : 11982 11982\n", "COVALENT_CYS : F\n", "NONBONDED_SEL_ATOMS : 1\n", "Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2410\n", "Dynamic pairs routine : 2, NATM x NATM cell sorting\n", "Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390\n", "LENNARD_JONES_SWITCH : 6.500 7.500\n", "COULOMB_JONES_SWITCH : 6.500 7.500\n", "RESIDUE_SPAN_RANGE : 0 99999\n", "NLOGN_USE : 15\n", "CONTACT_SHELL : 4.000\n", "DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F\n", "SPHERE_STDV : 0.050\n", "RADII_FACTOR : 0.820\n", "Current energy : 890.2857\n", "\n", "\n", "\n", "\n", "\n", "Summary of the restraint violations: \n", "\n", " NUM ... number of restraints.\n", " NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].\n", " RVIOL ... relative difference from the best value.\n", " NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].\n", " RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).\n", " RMS_2 ... RMS(feature, best_value, NUMB).\n", " MOL.PDF ... scaled contribution to -Ln(Molecular pdf).\n", "\n", " # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i\n", "------------------------------------------------------------------------------------------------------\n", " 1 Bond length potential : 1205 0 0 0.006 0.006 12.352 1.000\n", " 2 Bond angle potential : 1624 0 6 2.171 2.171 152.58 1.000\n", " 3 Stereochemical cosine torsion poten: 773 0 35 49.119 49.119 287.36 1.000\n", " 4 Stereochemical improper torsion pot: 506 0 1 1.584 1.584 26.643 1.000\n", " 5 Soft-sphere overlap restraints : 2410 0 0 0.002 0.002 0.88394 1.000\n", " 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000\n", " 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000\n", " 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000\n", " 9 Distance restraints 1 (CA-CA) : 2380 0 2 0.166 0.166 57.012 1.000\n", "10 Distance restraints 2 (N-O) : 2535 0 0 0.185 0.185 75.602 1.000\n", "11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "13 Mainchain Omega dihedral restraints: 146 0 1 4.287 4.287 31.647 1.000\n", "14 Sidechain Chi_1 dihedral restraints: 125 0 0 68.796 68.796 24.181 1.000\n", "15 Sidechain Chi_2 dihedral restraints: 98 0 0 70.106 70.106 36.112 1.000\n", "16 Sidechain Chi_3 dihedral restraints: 40 0 0 79.528 79.528 31.384 1.000\n", "17 Sidechain Chi_4 dihedral restraints: 19 0 0 90.345 90.345 12.927 1.000\n", "18 Disulfide distance restraints : 4 0 0 0.007 0.007 0.36999E-01 1.000\n", "19 Disulfide angle restraints : 8 0 0 1.723 1.723 0.52438 1.000\n", "20 Disulfide dihedral angle restraints: 4 0 0 29.770 29.770 3.3614 1.000\n", "21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "23 Distance restraints 3 (SDCH-MNCH) : 1577 0 0 0.438 0.438 27.315 1.000\n", "24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000\n", "25 Phi/Psi pair of dihedral restraints: 145 17 18 24.303 60.966 53.991 1.000\n", "26 Distance restraints 4 (SDCH-SDCH) : 793 0 1 0.705 0.705 56.375 1.000\n", "27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000\n", "28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000\n", "29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000\n", "30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000\n", "36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000\n", "37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000\n", "38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "\n", "\n", "\n", "# Heavy relative violation of each residue is written to: without_ligand.V99990002\n", "# The profile is NOT normalized by the number of restraints.\n", "# The profiles are smoothed over a window of residues: 1\n", "# The sum of all numbers in the file: 15682.0039\n", "\n", "\n", "\n", "List of the violated restraints:\n", " A restraint is violated when the relative difference\n", " from the best value (RVIOL) is larger than CUTOFF.\n", "\n", " ICSR ... index of a restraint in the current set.\n", " RESNO ... residue numbers of the first two atoms.\n", " ATM ... IUPAC atom names of the first two atoms.\n", " FEAT ... the value of the feature in the model.\n", " restr ... the mean of the basis restraint with the smallest\n", " difference from the model (local minimum).\n", " viol ... difference from the local minimum.\n", " rviol ... relative difference from the local minimum.\n", " RESTR ... the best value (global minimum).\n", " VIOL ... difference from the best value.\n", " RVIOL ... relative difference from the best value.\n", "\n", "\n", "-------------------------------------------------------------------------------------------------\n", "\n", "Feature 25 : Phi/Psi pair of dihedral restraints \n", "List of the RVIOL violations larger than : 6.5000\n", "\n", " # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL\n", " 1 4125 1M 2K C N 7 9 -63.80 -70.20 8.60 0.72 -62.90 173.05 22.52\n", " 1 2K 2K N CA 9 10 146.15 140.40 -40.80\n", " 2 4127 3V 4L C N 23 25 -92.58 -108.50 16.60 0.85 -63.50 -179.25 23.59\n", " 2 4L 4L N CA 25 26 137.19 132.50 -41.20\n", " 3 4128 4L 5L C N 31 33 -113.70 -108.50 27.66 1.43 -63.50 166.87 26.27\n", " 3 5L 5L N CA 33 34 159.66 132.50 -41.20\n", " 4 4129 5L 6L C N 39 41 -122.42 -108.50 14.54 0.65 -63.50 -172.61 23.39\n", " 4 6L 6L N CA 41 42 136.69 132.50 -41.20\n", " 5 4130 6L 7L C N 47 49 -93.57 -70.70 27.91 1.91 -63.50 163.98 24.59\n", " 5 7L 7L N CA 49 50 157.60 141.60 -41.20\n", " 6 4131 7L 8G C N 55 57 142.51 -167.20 50.98 0.80 82.20 -175.41 11.82\n", " 6 8G 8G N CA 57 58 -177.04 174.60 8.50\n", " 7 4132 8G 9F C N 59 61 -88.75 -71.40 75.80 6.51 -63.20 114.12 14.23\n", " 7 9F 9F N CA 61 62 66.92 140.70 -44.30\n", " 8 4134 10I 11F C N 78 80 -92.52 -71.40 53.32 4.70 -63.20 139.16 17.46\n", " 8 11F 11F N CA 80 81 91.74 140.70 -44.30\n", " 9 4136 12C 13S C N 95 97 -160.88 -136.60 34.52 1.12 -64.10 177.89 19.87\n", " 9 13S 13S N CA 97 98 175.73 151.20 -35.00\n", " 10 4137 13S 14M C N 101 103 -74.40 -73.00 20.38 1.35 -63.40 156.56 24.24\n", " 10 14M 14M N CA 103 104 163.33 143.00 -40.50\n", " 11 4138 14M 15A C N 109 111 -59.72 -68.20 37.16 2.70 -62.50 150.05 24.73\n", " 11 15A 15A N CA 111 112 109.13 145.30 -40.90\n", " 12 4139 15A 16A C N 114 116 152.02 -134.00 80.70 1.84 -62.50 -158.18 40.41\n", " 12 16A 16A N CA 116 117 179.23 147.00 -40.90\n", " 13 4140 16A 17H C N 119 121 70.70 56.30 95.74 9.74 -63.20 -137.46 36.25\n", " 13 17H 17H N CA 121 122 135.45 40.80 -42.30\n", " 14 4141 17H 18G C N 129 131 176.24 -167.20 16.92 0.26 82.20 -166.11 13.63\n", " 14 18G 18G N CA 131 132 178.06 174.60 8.50\n", " 15 4142 18G 19K C N 133 135 -91.47 -70.20 28.83 2.41 -62.90 164.24 19.94\n", " 15 19K 19K N CA 135 136 120.94 140.40 -40.80\n", " 16 4177 53E 54S C N 436 438 -137.42 -64.10 80.90 8.55 -64.10 80.90 8.55\n", " 16 54S 54S N CA 438 439 -0.81 -35.00 -35.00\n", " 17 4189 65P 66G C N 528 530 -68.85 -62.40 7.73 1.46 82.20 160.40 12.23\n", " 17 66G 66G N CA 530 531 -45.46 -41.20 8.50\n", "\n", "\n", "report______> Distribution of short non-bonded contacts:\n", "\n", "\n", "DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40\n", "DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50\n", "FREQUENCY: 0 0 0 0 1 4 13 49 70 112 115 128 154 201 199\n", "\n", "\n", "<< end of ENERGY.\n", "\n", ">> Summary of successfully produced models:\n", "Filename molpdf\n", "----------------------------------------\n", "without_ligand.B99990001.pdb 790.62006\n", "without_ligand.B99990002.pdb 890.28571\n", "\n" ] } ], "source": [ "s = alignm[0]\n", "pdb = alignm[1]\n", "\n", "print s.code, pdb.code\n", "\n", "## Создаем объект automodel\n", "a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns= pdb.code , sequence = s.code )\n", "\n", "a.name='mod'+s.code\n", "a.starting_model = 1\n", "a.ending_model = 2\n", "a.make()" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": false }, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "448efb3366a948bfb0a2aaaa49854769", "version_major": 2, "version_minor": 0 }, "text/html": [ "

Failed to display Jupyter Widget of type NGLWidget.

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\n", " If you're reading this message in Jupyter Notebook or JupyterLab, it may mean\n", " that the widgets JavaScript is still loading. If this message persists, it\n", " likely means that the widgets JavaScript library is either not installed or\n", " not enabled. See the Jupyter\n", " Widgets Documentation for setup instructions.\n", "

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\n" ], "text/plain": [ "NGLWidget()" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "nglview.show_structure_file('without_ligand.B99990001.pdb')" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": false }, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "910829b15e9342798071b6b51bfe7427", "version_major": 2, "version_minor": 0 }, "text/html": [ "

Failed to display Jupyter Widget of type NGLWidget.

\n", "

\n", " If you're reading this message in Jupyter Notebook or JupyterLab, it may mean\n", " that the widgets JavaScript is still loading. If this message persists, it\n", " likely means that the widgets JavaScript library is either not installed or\n", " not enabled. See the Jupyter\n", " Widgets Documentation for setup instructions.\n", "

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\n", " If you're reading this message in another notebook frontend (for example, a static\n", " rendering on GitHub or NBViewer),\n", " it may mean that your frontend doesn't currently support widgets.\n", "

\n" ], "text/plain": [ "NGLWidget()" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# original structure\n", "nglview.show_structure_file('1lmp.pdb')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Find ligand code" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " LYS VAL TYR ASP ARG CYS GLU LEU ALA ARG ALA LEU LYS ALA SER GLY MET ASP GLY TYR \n", " K V Y D R C E L A R A L K A S G M D G Y \n", " ALA GLY ASN SER LEU PRO ASN TRP VAL CYS LEU SER LYS TRP GLU SER SER TYR ASN THR \n", " A G N S L P N W V C L S K W E S S Y N T \n", " GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP TYR GLY ILE PHE GLN ILE ASN SER \n", " Q A T N R N T D G S T D Y G I F Q I N S \n", " ARG TYR TRP CYS ASP ASP GLY ARG THR PRO GLY ALA LYS ASN VAL CYS GLY ILE ARG CYS \n", " R Y W C D D G R T P G A K N V C G I R C \n", " SER GLN LEU LEU THR ASP ASP LEU THR VAL ALA ILE ARG CYS ALA LYS ARG VAL VAL LEU \n", " S Q L L T D D L T V A I R C A K R V V L \n", " ASP PRO ASN GLY ILE GLY ALA TRP VAL ALA TRP ARG LEU HIS CYS GLN ASN GLN ASP LEU \n", " D P N G I G A W V A W R L H C Q N Q D L \n", " ARG SER TYR VAL ALA GLY CYS GLY VAL NAG NAG NDG \n", " R S Y V A G C G V . . . \n" ] } ], "source": [ "n=20\n", "for i in range(0,len(alignm[1].residues),n):\n", " if (i+n) < len(alignm[1].residues):\n", " print str('{:^5}'*n).format(*[k.name for k in alignm[1].residues[i:i+n]])\n", " print str('{:^5}'*n).format(*[k.code for k in alignm[1].residues[i:i+n]])\n", " else:\n", " n = len(alignm[1].residues)-i\n", " print str('{:^5}'*n).format(*[k.name for k in alignm[1].residues[i:len(alignm[1].residues)]])\n", " print str('{:^5}'*n).format(*[k.code for k in alignm[1].residues[i:len(alignm[1].residues)]])" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": true }, "outputs": [], "source": [ "alignm2=modeller.alignment(env)\n", "residues = ''.join([k.code for k in alignm[0].residues]) + ''.join([k.code for k in alignm[1].residues[-3:]])\n", "alignm2.append_sequence(residues)\n", "## создадим модель\n", "mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))\n", "## и добавим в выравнивание\n", "alignm2.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')\n", "alignm2[0].code = 'with_ligand'" ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "SALIGN_____> adding the next group to the alignment; iteration 1\n", "with_ligand 1lmp\n", "automodel__W> Topology and/or parameter libraries already in memory. These will\n", " be used instead of the automodel defaults. If this is not what you\n", " want, clear them before creating the automodel object with\n", " env.libs.topology.clear() and env.libs.parameters.clear()\n", "fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA\n", " (This is usually caused by non-standard residues, such\n", " as ligands, or by PDB files with missing atoms.)\n", "fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA\n", " (This is usually caused by non-standard residues, such\n", " as ligands, or by PDB files with missing atoms.)\n", "\n", "check_ali___> Checking the sequence-structure alignment. \n", "\n", "Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:\n", "\n", "ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST\n", "----------------------------------------------\n", "END OF TABLE\n", "\n", "getf_______W> RTF restraint not found in the atoms list:\n", " residue type, indices: 10 147\n", " atom names : C +N\n", " atom indices : 1177 0\n", "\n", "getf_______W> RTF restraint not found in the atoms list:\n", " residue type, indices: 10 147\n", " atom names : C CA +N O\n", " atom indices : 1177 1172 0 1178\n", "fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA\n", " (This is usually caused by non-standard residues, such\n", " as ligands, or by PDB files with missing atoms.)\n", "patch_s_522_> Number of disulfides patched in MODEL: 4\n", "mdtrsr__446W> A potential that relies on one protein is used, yet you have at\n", " least one known structure available. MDT, not library, potential is used.\n", "iup2crm_280W> No topology library in memory or assigning a BLK residue.\n", " Default CHARMM atom type assigned: C1 --> CT2\n", " This message is written only for the first such atom.\n", "43 atoms in HETATM/BLK residues constrained\n", "to protein atoms within 2.30 angstroms\n", "and protein CA atoms within 10.00 angstroms\n", "43 atoms in residues without defined topology\n", "constrained to be rigid bodies\n", "condens_443_> Restraints marked for deletion were removed.\n", " Total number of restraints before, now: 14413 13381\n", "iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.\n", "\n", "\n", ">> ENERGY; Differences between the model's features and restraints:\n", "Number of all residues in MODEL : 150\n", "Number of all, selected real atoms : 1222 1222\n", "Number of all, selected pseudo atoms : 0 0\n", "Number of all static, selected restraints : 13381 13381\n", "COVALENT_CYS : F\n", "NONBONDED_SEL_ATOMS : 1\n", "Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2608\n", "Dynamic pairs routine : 2, NATM x NATM cell sorting\n", "Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390\n", "LENNARD_JONES_SWITCH : 6.500 7.500\n", "COULOMB_JONES_SWITCH : 6.500 7.500\n", "RESIDUE_SPAN_RANGE : 0 99999\n", "NLOGN_USE : 15\n", "CONTACT_SHELL : 4.000\n", "DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F\n", "SPHERE_STDV : 0.050\n", "RADII_FACTOR : 0.820\n", "Current energy : 986.9169\n", "\n", "\n", "\n", "\n", "\n", "Summary of the restraint violations: \n", "\n", " NUM ... number of restraints.\n", " NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].\n", " RVIOL ... relative difference from the best value.\n", " NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].\n", " RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).\n", " RMS_2 ... RMS(feature, best_value, NUMB).\n", " MOL.PDF ... scaled contribution to -Ln(Molecular pdf).\n", "\n", " # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i\n", "------------------------------------------------------------------------------------------------------\n", " 1 Bond length potential : 1205 0 0 0.007 0.007 17.018 1.000\n", " 2 Bond angle potential : 1624 0 6 2.201 2.201 157.57 1.000\n", " 3 Stereochemical cosine torsion poten: 773 0 36 49.331 49.331 288.41 1.000\n", " 4 Stereochemical improper torsion pot: 506 0 1 1.544 1.544 25.815 1.000\n", " 5 Soft-sphere overlap restraints : 2608 2 2 0.008 0.008 17.726 1.000\n", " 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000\n", " 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000\n", " 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000\n", " 9 Distance restraints 1 (CA-CA) : 2380 0 0 0.134 0.134 42.382 1.000\n", "10 Distance restraints 2 (N-O) : 2535 0 0 0.180 0.180 77.130 1.000\n", "11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "13 Mainchain Omega dihedral restraints: 146 0 1 4.076 4.076 28.608 1.000\n", "14 Sidechain Chi_1 dihedral restraints: 125 0 4 77.022 77.022 40.143 1.000\n", "15 Sidechain Chi_2 dihedral restraints: 98 0 2 83.185 83.185 50.228 1.000\n", "16 Sidechain Chi_3 dihedral restraints: 40 0 0 82.143 82.143 29.844 1.000\n", "17 Sidechain Chi_4 dihedral restraints: 19 0 0 88.836 88.836 12.418 1.000\n", "18 Disulfide distance restraints : 4 0 0 0.015 0.015 0.15137 1.000\n", "19 Disulfide angle restraints : 8 0 0 2.254 2.254 0.89779 1.000\n", "20 Disulfide dihedral angle restraints: 4 0 0 23.797 23.797 2.2068 1.000\n", "21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "23 Distance restraints 3 (SDCH-MNCH) : 1577 0 0 0.426 0.426 44.445 1.000\n", "24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000\n", "25 Phi/Psi pair of dihedral restraints: 145 18 18 22.873 62.767 54.413 1.000\n", "26 Distance restraints 4 (SDCH-SDCH) : 793 0 1 0.777 0.777 76.270 1.000\n", "27 Distance restraints 5 (X-Y) : 1399 0 0 0.042 0.042 21.236 1.000\n", "28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000\n", "29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000\n", "30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000\n", "36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000\n", "37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000\n", "38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "\n", "\n", "\n", "# Heavy relative violation of each residue is written to: with_ligand.V99990001\n", "# The profile is NOT normalized by the number of restraints.\n", "# The profiles are smoothed over a window of residues: 1\n", "# The sum of all numbers in the file: 17066.4570\n", "\n", "\n", "\n", "List of the violated restraints:\n", " A restraint is violated when the relative difference\n", " from the best value (RVIOL) is larger than CUTOFF.\n", "\n", " ICSR ... index of a restraint in the current set.\n", " RESNO ... residue numbers of the first two atoms.\n", " ATM ... IUPAC atom names of the first two atoms.\n", " FEAT ... the value of the feature in the model.\n", " restr ... the mean of the basis restraint with the smallest\n", " difference from the model (local minimum).\n", " viol ... difference from the local minimum.\n", " rviol ... relative difference from the local minimum.\n", " RESTR ... the best value (global minimum).\n", " VIOL ... difference from the best value.\n", " RVIOL ... relative difference from the best value.\n", "\n", "\n", "-------------------------------------------------------------------------------------------------\n", "\n", "Feature 25 : Phi/Psi pair of dihedral restraints \n", "List of the RVIOL violations larger than : 6.5000\n", "\n", " # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL\n", " 1 4125 1M 2K C N 7 9 -82.94 -70.20 16.36 0.99 -62.90 169.72 23.19\n", " 1 2K 2K N CA 9 10 150.67 140.40 -40.80\n", " 2 4127 3V 4L C N 23 25 -71.22 -70.70 4.60 0.33 -63.50 172.80 24.44\n", " 2 4L 4L N CA 25 26 146.17 141.60 -41.20\n", " 3 4128 4L 5L C N 31 33 -66.46 -70.70 4.67 0.47 -63.50 175.26 24.50\n", " 3 5L 5L N CA 33 34 143.56 141.60 -41.20\n", " 4 4129 5L 6L C N 39 41 -68.34 -70.70 3.34 0.21 -63.50 179.63 25.22\n", " 4 6L 6L N CA 41 42 139.23 141.60 -41.20\n", " 5 4130 6L 7L C N 47 49 -74.07 -70.70 3.42 0.29 -63.50 176.95 25.19\n", " 5 7L 7L N CA 49 50 142.17 141.60 -41.20\n", " 6 4131 7L 8G C N 55 57 130.25 78.70 52.50 2.38 82.20 -178.09 11.15\n", " 6 8G 8G N CA 57 58 -176.04 -166.10 8.50\n", " 7 4132 8G 9F C N 59 61 -75.74 -71.40 4.34 0.29 -63.20 175.50 25.21\n", " 7 9F 9F N CA 61 62 140.65 140.70 -44.30\n", " 8 4134 10I 11F C N 78 80 -129.14 -124.20 5.80 0.15 -63.20 -178.26 29.57\n", " 8 11F 11F N CA 80 81 146.35 143.30 -44.30\n", " 9 4136 12C 13S C N 95 97 -68.42 -72.40 25.93 1.39 -64.10 161.84 11.48\n", " 9 13S 13S N CA 97 98 126.78 152.40 -35.00\n", " 10 4137 13S 14M C N 101 103 -171.86 -125.60 49.01 1.57 -63.40 -164.36 37.47\n", " 10 14M 14M N CA 103 104 156.68 140.50 -40.50\n", " 11 4138 14M 15A C N 109 111 -89.38 -68.20 42.27 4.05 -62.50 152.02 23.74\n", " 11 15A 15A N CA 111 112 108.72 145.30 -40.90\n", " 12 4139 15A 16A C N 114 116 169.77 -134.00 63.01 1.44 -62.50 -167.76 38.09\n", " 12 16A 16A N CA 116 117 175.43 147.00 -40.90\n", " 13 4140 16A 17H C N 119 121 -136.55 -125.60 67.93 2.36 -63.20 133.77 21.41\n", " 13 17H 17H N CA 121 122 -154.16 138.80 -42.30\n", " 14 4141 17H 18G C N 129 131 -76.19 -80.20 4.78 0.35 82.20 -128.97 7.00\n", " 14 18G 18G N CA 131 132 176.69 174.10 8.50\n", " 15 4142 18G 19K C N 133 135 -71.64 -70.20 14.31 1.07 -62.90 167.19 21.25\n", " 15 19K 19K N CA 135 136 126.16 140.40 -40.80\n", " 16 4177 53E 54S C N 436 438 -136.45 -64.10 80.20 8.42 -64.10 80.20 8.42\n", " 16 54S 54S N CA 438 439 -0.39 -35.00 -35.00\n", " 17 4188 64N 65P C N 521 523 -76.69 -64.50 13.49 1.09 -58.70 177.44 16.14\n", " 17 65P 65P N CA 523 524 152.98 147.20 -30.50\n", " 18 4241 117I 118V C N 932 934 -56.39 -62.40 50.23 6.72 -62.40 50.23 6.72\n", " 18 118V 118V N CA 934 935 7.47 -42.40 -42.40\n", "\n", "\n", "report______> Distribution of short non-bonded contacts:\n", "\n", "\n", "DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40\n", "DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50\n", "FREQUENCY: 0 0 0 0 1 12 14 55 76 137 129 155 177 183 210\n", "\n", "\n", "<< end of ENERGY.\n", "\n", "\n", ">> ENERGY; Differences between the model's features and restraints:\n", "Number of all residues in MODEL : 150\n", "Number of all, selected real atoms : 1222 1222\n", "Number of all, selected pseudo atoms : 0 0\n", "Number of all static, selected restraints : 13381 13381\n", "COVALENT_CYS : F\n", "NONBONDED_SEL_ATOMS : 1\n", "Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2608\n", "Dynamic pairs routine : 2, NATM x NATM cell sorting\n", "Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390\n", "LENNARD_JONES_SWITCH : 6.500 7.500\n", "COULOMB_JONES_SWITCH : 6.500 7.500\n", "RESIDUE_SPAN_RANGE : 0 99999\n", "NLOGN_USE : 15\n", "CONTACT_SHELL : 4.000\n", "DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F\n", "SPHERE_STDV : 0.050\n", "RADII_FACTOR : 0.820\n", "Current energy : 963.2237\n", "\n", "\n", "\n", "\n", "\n", "Summary of the restraint violations: \n", "\n", " NUM ... number of restraints.\n", " NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].\n", " RVIOL ... relative difference from the best value.\n", " NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].\n", " RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).\n", " RMS_2 ... RMS(feature, best_value, NUMB).\n", " MOL.PDF ... scaled contribution to -Ln(Molecular pdf).\n", "\n", " # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i\n", "------------------------------------------------------------------------------------------------------\n", " 1 Bond length potential : 1205 0 0 0.007 0.007 17.632 1.000\n", " 2 Bond angle potential : 1624 0 8 2.242 2.242 164.34 1.000\n", " 3 Stereochemical cosine torsion poten: 773 0 33 49.416 49.416 289.20 1.000\n", " 4 Stereochemical improper torsion pot: 506 0 0 1.479 1.479 23.834 1.000\n", " 5 Soft-sphere overlap restraints : 2608 2 2 0.008 0.008 18.277 1.000\n", " 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000\n", " 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000\n", " 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000\n", " 9 Distance restraints 1 (CA-CA) : 2380 0 0 0.131 0.131 40.823 1.000\n", "10 Distance restraints 2 (N-O) : 2535 0 0 0.178 0.178 74.743 1.000\n", "11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "13 Mainchain Omega dihedral restraints: 146 0 2 4.473 4.473 34.453 1.000\n", "14 Sidechain Chi_1 dihedral restraints: 125 0 2 67.065 67.065 25.521 1.000\n", "15 Sidechain Chi_2 dihedral restraints: 98 0 4 70.929 70.929 44.676 1.000\n", "16 Sidechain Chi_3 dihedral restraints: 40 0 0 69.402 69.402 23.443 1.000\n", "17 Sidechain Chi_4 dihedral restraints: 19 0 0 86.281 86.281 13.620 1.000\n", "18 Disulfide distance restraints : 4 0 0 0.006 0.006 0.25204E-01 1.000\n", "19 Disulfide angle restraints : 8 0 0 2.636 2.636 1.2271 1.000\n", "20 Disulfide dihedral angle restraints: 4 0 0 26.145 26.145 2.6144 1.000\n", "21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "23 Distance restraints 3 (SDCH-MNCH) : 1577 0 0 0.379 0.379 38.241 1.000\n", "24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000\n", "25 Phi/Psi pair of dihedral restraints: 145 17 20 22.629 60.754 58.389 1.000\n", "26 Distance restraints 4 (SDCH-SDCH) : 793 0 0 0.720 0.720 70.342 1.000\n", "27 Distance restraints 5 (X-Y) : 1399 0 0 0.042 0.042 21.824 1.000\n", "28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000\n", "29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000\n", "30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000\n", "36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000\n", "37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000\n", "38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "\n", "\n", "\n", "# Heavy relative violation of each residue is written to: with_ligand.V99990002\n", "# The profile is NOT normalized by the number of restraints.\n", "# The profiles are smoothed over a window of residues: 1\n", "# The sum of all numbers in the file: 15741.5723\n", "\n", "\n", "\n", "List of the violated restraints:\n", " A restraint is violated when the relative difference\n", " from the best value (RVIOL) is larger than CUTOFF.\n", "\n", " ICSR ... index of a restraint in the current set.\n", " RESNO ... residue numbers of the first two atoms.\n", " ATM ... IUPAC atom names of the first two atoms.\n", " FEAT ... the value of the feature in the model.\n", " restr ... the mean of the basis restraint with the smallest\n", " difference from the model (local minimum).\n", " viol ... difference from the local minimum.\n", " rviol ... relative difference from the local minimum.\n", " RESTR ... the best value (global minimum).\n", " VIOL ... difference from the best value.\n", " RVIOL ... relative difference from the best value.\n", "\n", "\n", "-------------------------------------------------------------------------------------------------\n", "\n", "Feature 25 : Phi/Psi pair of dihedral restraints \n", "List of the RVIOL violations larger than : 6.5000\n", "\n", " # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL\n", " 1 4125 1M 2K C N 7 9 -81.14 -70.20 17.55 1.05 -62.90 166.10 22.61\n", " 1 2K 2K N CA 9 10 154.11 140.40 -40.80\n", " 2 4127 3V 4L C N 23 25 -114.08 -108.50 17.45 0.87 -63.50 177.14 27.71\n", " 2 4L 4L N CA 25 26 149.03 132.50 -41.20\n", " 3 4128 4L 5L C N 31 33 -70.68 -70.70 11.10 0.84 -63.50 166.25 23.50\n", " 3 5L 5L N CA 33 34 152.70 141.60 -41.20\n", " 4 4129 5L 6L C N 39 41 -64.48 -70.70 6.54 0.52 -63.50 179.23 24.94\n", " 4 6L 6L N CA 41 42 139.57 141.60 -41.20\n", " 5 4130 6L 7L C N 47 49 -99.59 -108.50 8.99 0.44 -63.50 178.57 22.98\n", " 5 7L 7L N CA 49 50 133.68 132.50 -41.20\n", " 6 4131 7L 8G C N 55 57 -167.53 -167.20 47.77 1.88 82.20 161.74 12.32\n", " 6 8G 8G N CA 57 58 126.83 174.60 8.50\n", " 7 4132 8G 9F C N 59 61 -175.75 -124.20 60.56 1.59 -63.20 -179.89 31.72\n", " 7 9F 9F N CA 61 62 175.08 143.30 -44.30\n", " 8 4134 10I 11F C N 78 80 -83.49 -71.40 40.43 3.52 -63.20 147.82 19.20\n", " 8 11F 11F N CA 80 81 102.12 140.70 -44.30\n", " 9 4136 12C 13S C N 95 97 -74.99 -72.40 16.62 0.89 -64.10 156.56 12.02\n", " 9 13S 13S N CA 97 98 168.82 152.40 -35.00\n", " 10 4137 13S 14M C N 101 103 -82.45 -73.00 71.37 4.99 -63.40 114.36 15.69\n", " 10 14M 14M N CA 103 104 72.26 143.00 -40.50\n", " 11 4138 14M 15A C N 109 111 -163.05 -134.00 29.64 0.78 -62.50 -165.70 37.20\n", " 11 15A 15A N CA 111 112 152.85 147.00 -40.90\n", " 12 4139 15A 16A C N 114 116 -64.85 -68.20 7.53 0.50 -62.50 179.47 29.30\n", " 12 16A 16A N CA 116 117 138.56 145.30 -40.90\n", " 13 4140 16A 17H C N 119 121 -136.06 -125.60 11.58 0.49 -63.20 -169.40 20.48\n", " 13 17H 17H N CA 121 122 133.82 138.80 -42.30\n", " 14 4141 17H 18G C N 129 131 -176.17 -167.20 19.38 0.79 82.20 -179.71 13.15\n", " 14 18G 18G N CA 131 132 157.42 174.60 8.50\n", " 15 4142 18G 19K C N 133 135 -81.94 -70.20 17.34 1.45 -62.90 169.51 21.04\n", " 15 19K 19K N CA 135 136 127.63 140.40 -40.80\n", " 16 4177 53E 54S C N 436 438 -134.90 -64.10 74.64 8.43 -64.10 74.64 8.43\n", " 16 54S 54S N CA 438 439 -11.35 -35.00 -35.00\n", " 17 4188 64N 65P C N 521 523 -76.19 -64.50 14.43 1.02 -58.70 174.73 15.88\n", " 17 65P 65P N CA 523 524 155.65 147.20 -30.50\n", "\n", "\n", "report______> Distribution of short non-bonded contacts:\n", "\n", "\n", "DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40\n", "DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50\n", "FREQUENCY: 0 0 0 0 1 8 13 58 85 144 124 137 193 197 192\n", "\n", "\n", "<< end of ENERGY.\n", "\n", ">> Summary of successfully produced models:\n", "Filename molpdf\n", "----------------------------------------\n", "with_ligand.B99990001.pdb 986.91687\n", "with_ligand.B99990002.pdb 963.22369\n", "\n" ] } ], "source": [ "alignm2.salign()\n", "alignm2.write(file='all_in_one_ligand.ali', alignment_format='PIR')\n", "s = alignm2[0]\n", "pdb = alignm2[1]\n", "\n", "print s.code, pdb.code\n", "\n", "## Создаем объект automodel\n", "a = modeller.automodel.automodel(env, alnfile='all_in_one_ligand.ali', knowns= pdb.code , sequence = s.code )\n", "\n", "a.name='mod'+s.code\n", "a.starting_model = 1\n", "a.ending_model = 2\n", "a.make()" ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "collapsed": false }, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "a0c369ee92ef4e68974345123186bd32", "version_major": 2, "version_minor": 0 }, "text/html": [ "

Failed to display Jupyter Widget of type NGLWidget.

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\n", " If you're reading this message in Jupyter Notebook or JupyterLab, it may mean\n", " that the widgets JavaScript is still loading. If this message persists, it\n", " likely means that the widgets JavaScript library is either not installed or\n", " not enabled. See the Jupyter\n", " Widgets Documentation for setup instructions.\n", "

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\n", " If you're reading this message in another notebook frontend (for example, a static\n", " rendering on GitHub or NBViewer),\n", " it may mean that your frontend doesn't currently support widgets.\n", "

\n" ], "text/plain": [ "NGLWidget()" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "nglview.show_structure_file('with_ligand.B99990001.pdb')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Restrains" ] }, { "cell_type": "code", "execution_count": 67, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "['R 3 1 1 1 2 2 1 100 99 1.4200 0.0263 \\n', 'R 3 1 1 1 2 2 1 97 98 1.4300 0.0304 \\n', 'R 3 1 1 1 2 2 1 102 101 1.2300 0.0218 \\n', 'R 3 1 1 1 2 2 1 101 98 1.4900 0.0344 \\n', 'R 3 1 1 1 2 2 1 101 103 1.3450 0.0282 \\n', 'R 3 1 1 1 2 2 1 105 104 1.5380 0.0364 \\n', 'R 3 1 1 1 2 2 1 106 105 1.5300 0.0364 \\n', 'R 3 1 1 1 2 2 1 107 106 1.8180 0.0386 \\n', 'R 3 1 1 1 2 2 1 108 107 1.8160 0.0351 \\n', 'R 3 1 1 1 2 2 1 103 104 1.4300 0.0304 \\n', 'R 3 1 1 1 2 2 1 110 109 1.2300 0.0218 \\n', 'R 3 1 1 1 2 2 1 109 104 1.4900 0.0344 \\n', 'R 3 1 1 1 2 2 1 109 111 1.3450 0.0282 \\n', 'R 3 1 1 1 2 2 1 113 112 1.5380 0.0364 \\n', 'R 3 1 1 1 2 2 1 111 112 1.4300 0.0304 \\n', 'R 3 1 1 1 2 2 1 115 114 1.2300 0.0218 \\n', 'R 3 1 1 1 2 2 1 114 112 1.4900 0.0344 \\n', 'R 3 1 1 1 2 2 1 114 116 1.3450 0.0282 \\n', 'R 3 1 1 1 2 2 1 118 117 1.5380 0.0364 \\n']\n" ] } ], "source": [ "with open('with_ligand.rsr') as fn:\n", " lines = fn.readlines()\n", "print(lines[100:119])" ] }, { "cell_type": "code", "execution_count": 72, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "automodel__W> Topology and/or parameter libraries already in memory. These will\n", " be used instead of the automodel defaults. If this is not what you\n", " want, clear them before creating the automodel object with\n", " env.libs.topology.clear() and env.libs.parameters.clear()\n", "fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA\n", " (This is usually caused by non-standard residues, such\n", " as ligands, or by PDB files with missing atoms.)\n", "fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA\n", " (This is usually caused by non-standard residues, such\n", " as ligands, or by PDB files with missing atoms.)\n", "\n", "check_ali___> Checking the sequence-structure alignment. \n", "\n", "Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:\n", "\n", "ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST\n", "----------------------------------------------\n", "END OF TABLE\n", "\n", "getf_______W> RTF restraint not found in the atoms list:\n", " residue type, indices: 10 147\n", " atom names : C +N\n", " atom indices : 1177 0\n", "\n", "getf_______W> RTF restraint not found in the atoms list:\n", " residue type, indices: 10 147\n", " atom names : C CA +N O\n", " atom indices : 1177 1172 0 1178\n", "fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA\n", " (This is usually caused by non-standard residues, such\n", " as ligands, or by PDB files with missing atoms.)\n", "patch_s_522_> Number of disulfides patched in MODEL: 4\n", "mdtrsr__446W> A potential that relies on one protein is used, yet you have at\n", " least one known structure available. MDT, not library, potential is used.\n", "iup2crm_280W> No topology library in memory or assigning a BLK residue.\n", " Default CHARMM atom type assigned: C1 --> CT2\n", " This message is written only for the first such atom.\n", "43 atoms in HETATM/BLK residues constrained\n", "to protein atoms within 2.30 angstroms\n", "and protein CA atoms within 10.00 angstroms\n", "43 atoms in residues without defined topology\n", "constrained to be rigid bodies\n", "runcmd_____W>: creation of new member 'my_data' in : possible typo!\n", "condens_443_> Restraints marked for deletion were removed.\n", " Total number of restraints before, now: 14414 13382\n", "\n", "\n", ">> ENERGY; Differences between the model's features and restraints:\n", "Number of all residues in MODEL : 150\n", "Number of all, selected real atoms : 1222 1222\n", "Number of all, selected pseudo atoms : 0 0\n", "Number of all static, selected restraints : 13382 13382\n", "COVALENT_CYS : F\n", "NONBONDED_SEL_ATOMS : 1\n", "Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2585\n", "Dynamic pairs routine : 2, NATM x NATM cell sorting\n", "Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390\n", "LENNARD_JONES_SWITCH : 6.500 7.500\n", "COULOMB_JONES_SWITCH : 6.500 7.500\n", "RESIDUE_SPAN_RANGE : 0 99999\n", "NLOGN_USE : 15\n", "CONTACT_SHELL : 4.000\n", "DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F\n", "SPHERE_STDV : 0.050\n", "RADII_FACTOR : 0.820\n", "Current energy : 2246.6326\n", "\n", "\n", "\n", "\n", "\n", "Summary of the restraint violations: \n", "\n", " NUM ... number of restraints.\n", " NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].\n", " RVIOL ... relative difference from the best value.\n", " NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].\n", " RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).\n", " RMS_2 ... RMS(feature, best_value, NUMB).\n", " MOL.PDF ... scaled contribution to -Ln(Molecular pdf).\n", "\n", " # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i\n", "------------------------------------------------------------------------------------------------------\n", " 1 Bond length potential : 1205 0 0 0.007 0.007 17.858 1.000\n", " 2 Bond angle potential : 1624 0 7 2.158 2.158 151.16 1.000\n", " 3 Stereochemical cosine torsion poten: 773 0 36 49.119 49.119 285.18 1.000\n", " 4 Stereochemical improper torsion pot: 506 0 0 1.369 1.369 21.554 1.000\n", " 5 Soft-sphere overlap restraints : 2585 2 3 0.012 0.012 43.782 1.000\n", " 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000\n", " 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000\n", " 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000\n", " 9 Distance restraints 1 (CA-CA) : 2380 0 0 0.130 0.130 41.306 1.000\n", "10 Distance restraints 2 (N-O) : 2535 0 0 0.182 0.182 78.892 1.000\n", "11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "13 Mainchain Omega dihedral restraints: 146 0 1 4.305 4.305 31.904 1.000\n", "14 Sidechain Chi_1 dihedral restraints: 125 0 1 70.547 70.547 33.279 1.000\n", "15 Sidechain Chi_2 dihedral restraints: 98 0 0 76.072 76.072 44.232 1.000\n", "16 Sidechain Chi_3 dihedral restraints: 40 0 0 78.179 78.179 28.371 1.000\n", "17 Sidechain Chi_4 dihedral restraints: 19 0 0 74.354 74.354 11.022 1.000\n", "18 Disulfide distance restraints : 4 0 0 0.007 0.007 0.37925E-01 1.000\n", "19 Disulfide angle restraints : 8 0 0 2.884 2.884 1.4697 1.000\n", "20 Disulfide dihedral angle restraints: 4 0 0 27.393 27.393 2.7304 1.000\n", "21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "23 Distance restraints 3 (SDCH-MNCH) : 1577 0 0 0.394 0.394 34.870 1.000\n", "24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000\n", "25 Phi/Psi pair of dihedral restraints: 145 17 17 22.542 60.192 57.289 1.000\n", "26 Distance restraints 4 (SDCH-SDCH) : 793 0 1 0.729 0.729 61.817 1.000\n", "27 Distance restraints 5 (X-Y) : 1400 3 17 0.194 0.194 1299.9 1.000\n", "28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000\n", "29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000\n", "30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000\n", "36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000\n", "37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000\n", "38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "\n", "\n", "\n", "# Heavy relative violation of each residue is written to: with_ligand.V99990001\n", "# The profile is NOT normalized by the number of restraints.\n", "# The profiles are smoothed over a window of residues: 1\n", "# The sum of all numbers in the file: 17283.4844\n", "\n", "\n", "\n", "List of the violated restraints:\n", " A restraint is violated when the relative difference\n", " from the best value (RVIOL) is larger than CUTOFF.\n", "\n", " ICSR ... index of a restraint in the current set.\n", " RESNO ... residue numbers of the first two atoms.\n", " ATM ... IUPAC atom names of the first two atoms.\n", " FEAT ... the value of the feature in the model.\n", " restr ... the mean of the basis restraint with the smallest\n", " difference from the model (local minimum).\n", " viol ... difference from the local minimum.\n", " rviol ... relative difference from the local minimum.\n", " RESTR ... the best value (global minimum).\n", " VIOL ... difference from the best value.\n", " RVIOL ... relative difference from the best value.\n", "\n", "\n", "-------------------------------------------------------------------------------------------------\n", "\n", "Feature 25 : Phi/Psi pair of dihedral restraints \n", "List of the RVIOL violations larger than : 6.5000\n", "\n", " # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL\n", " 1 4125 1M 2K C N 7 9 -91.11 -70.20 24.57 1.51 -62.90 168.29 23.49\n", " 1 2K 2K N CA 9 10 153.29 140.40 -40.80\n", " 2 4127 3V 4L C N 23 25 -66.28 -70.70 4.71 0.37 -63.50 178.88 25.00\n", " 2 4L 4L N CA 25 26 139.95 141.60 -41.20\n", " 3 4128 4L 5L C N 31 33 -122.63 -108.50 29.61 1.42 -63.50 170.83 27.38\n", " 3 5L 5L N CA 33 34 158.52 132.50 -41.20\n", " 4 4129 5L 6L C N 39 41 -72.71 -70.70 26.69 1.95 -63.50 150.87 21.49\n", " 4 6L 6L N CA 41 42 168.21 141.60 -41.20\n", " 5 4130 6L 7L C N 47 49 -60.44 -70.70 10.82 0.86 -63.50 179.39 25.08\n", " 5 7L 7L N CA 49 50 138.16 141.60 -41.20\n", " 6 4131 7L 8G C N 55 57 95.69 78.70 44.61 0.69 82.20 144.77 7.70\n", " 6 8G 8G N CA 57 58 152.65 -166.10 8.50\n", " 7 4132 8G 9F C N 59 61 -95.76 -71.40 59.84 5.28 -63.20 134.36 16.61\n", " 7 9F 9F N CA 61 62 86.05 140.70 -44.30\n", " 8 4134 10I 11F C N 78 80 -80.76 -71.40 12.85 0.74 -63.20 167.12 24.39\n", " 8 11F 11F N CA 80 81 149.51 140.70 -44.30\n", " 9 4136 12C 13S C N 95 97 -168.96 -136.60 44.58 1.42 -64.10 177.43 20.42\n", " 9 13S 13S N CA 97 98 -178.13 151.20 -35.00\n", " 10 4137 13S 14M C N 101 103 -87.69 -73.00 40.93 3.03 -63.40 147.31 20.22\n", " 10 14M 14M N CA 103 104 104.79 143.00 -40.50\n", " 11 4138 14M 15A C N 109 111 -161.80 -134.00 29.34 0.69 -62.50 -169.36 36.53\n", " 11 15A 15A N CA 111 112 156.36 147.00 -40.90\n", " 12 4139 15A 16A C N 114 116 -161.14 -134.00 30.58 0.70 -62.50 -173.74 35.77\n", " 12 16A 16A N CA 116 117 161.10 147.00 -40.90\n", " 13 4140 16A 17H C N 119 121 -71.21 -67.60 10.82 0.72 -63.20 167.68 21.47\n", " 13 17H 17H N CA 121 122 150.21 140.00 -42.30\n", " 14 4141 17H 18G C N 129 131 157.56 -167.20 35.71 0.83 82.20 177.16 12.06\n", " 14 18G 18G N CA 131 132 168.84 174.60 8.50\n", " 15 4142 18G 19K C N 133 135 -118.65 -118.00 10.45 0.50 -62.90 178.59 26.51\n", " 15 19K 19K N CA 135 136 149.54 139.10 -40.80\n", " 16 4177 53E 54S C N 436 438 -137.19 -64.10 78.62 8.61 -64.10 78.62 8.61\n", " 16 54S 54S N CA 438 439 -6.04 -35.00 -35.00\n", " 17 4188 64N 65P C N 521 523 -71.92 -64.50 12.82 1.34 -58.70 167.77 12.82\n", " 17 65P 65P N CA 523 524 136.75 147.20 -30.50\n", "\n", "-------------------------------------------------------------------------------------------------\n", "\n", "Feature 27 : Distance restraints 5 (X-Y) \n", "List of the RVIOL violations larger than : 4.5000\n", "\n", " # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL\n", " 1 13382 148. 150. C1 O1L 1180 1222 9.16 3.00 6.16 61.56 3.00 6.16 61.56\n", "\n", "\n", "report______> Distribution of short non-bonded contacts:\n", "\n", " serious non-bonded atom clash: 1180 1197 2.294\n", "\n", "DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40\n", "DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50\n", "FREQUENCY: 0 0 1 0 2 6 9 59 92 121 131 144 188 197 205\n", "\n", "\n", "<< end of ENERGY.\n", "iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.\n", "\n", "\n", ">> ENERGY; Differences between the model's features and restraints:\n", "Number of all residues in MODEL : 150\n", "Number of all, selected real atoms : 1222 1222\n", "Number of all, selected pseudo atoms : 0 0\n", "Number of all static, selected restraints : 13382 13382\n", "COVALENT_CYS : F\n", "NONBONDED_SEL_ATOMS : 1\n", "Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2761\n", "Dynamic pairs routine : 2, NATM x NATM cell sorting\n", "Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390\n", "LENNARD_JONES_SWITCH : 6.500 7.500\n", "COULOMB_JONES_SWITCH : 6.500 7.500\n", "RESIDUE_SPAN_RANGE : 0 99999\n", "NLOGN_USE : 15\n", "CONTACT_SHELL : 4.000\n", "DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F\n", "SPHERE_STDV : 0.050\n", "RADII_FACTOR : 0.820\n", "Current energy : 2485.3855\n", "\n", "\n", "\n", "\n", "\n", "Summary of the restraint violations: \n", "\n", " NUM ... number of restraints.\n", " NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].\n", " RVIOL ... relative difference from the best value.\n", " NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].\n", " RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).\n", " RMS_2 ... RMS(feature, best_value, NUMB).\n", " MOL.PDF ... scaled contribution to -Ln(Molecular pdf).\n", "\n", " # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i\n", "------------------------------------------------------------------------------------------------------\n", " 1 Bond length potential : 1205 0 0 0.008 0.008 20.348 1.000\n", " 2 Bond angle potential : 1624 1 13 2.369 2.369 184.07 1.000\n", " 3 Stereochemical cosine torsion poten: 773 0 39 49.523 49.523 298.82 1.000\n", " 4 Stereochemical improper torsion pot: 506 0 0 1.354 1.354 21.402 1.000\n", " 5 Soft-sphere overlap restraints : 2761 2 3 0.012 0.012 44.627 1.000\n", " 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000\n", " 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000\n", " 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000\n", " 9 Distance restraints 1 (CA-CA) : 2380 0 0 0.146 0.146 57.730 1.000\n", "10 Distance restraints 2 (N-O) : 2535 5 21 0.265 0.265 183.61 1.000\n", "11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "13 Mainchain Omega dihedral restraints: 146 0 4 4.999 4.999 43.024 1.000\n", "14 Sidechain Chi_1 dihedral restraints: 125 0 1 69.404 69.404 34.735 1.000\n", "15 Sidechain Chi_2 dihedral restraints: 98 0 1 71.129 71.129 42.556 1.000\n", "16 Sidechain Chi_3 dihedral restraints: 40 0 0 81.587 81.587 27.545 1.000\n", "17 Sidechain Chi_4 dihedral restraints: 19 0 0 105.660 105.660 15.359 1.000\n", "18 Disulfide distance restraints : 4 0 0 0.008 0.008 0.43987E-01 1.000\n", "19 Disulfide angle restraints : 8 0 0 3.443 3.443 2.0943 1.000\n", "20 Disulfide dihedral angle restraints: 4 0 0 24.596 24.596 2.0601 1.000\n", "21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "23 Distance restraints 3 (SDCH-MNCH) : 1577 0 0 0.412 0.412 39.042 1.000\n", "24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000\n", "25 Phi/Psi pair of dihedral restraints: 145 21 19 26.783 65.931 86.711 1.000\n", "26 Distance restraints 4 (SDCH-SDCH) : 793 0 4 0.853 0.853 86.460 1.000\n", "27 Distance restraints 5 (X-Y) : 1400 3 16 0.196 0.196 1295.1 1.000\n", "28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000\n", "29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000\n", "30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000\n", "36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000\n", "37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000\n", "38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000\n", "\n", "\n", "\n", "# Heavy relative violation of each residue is written to: with_ligand.V99990002\n", "# The profile is NOT normalized by the number of restraints.\n", "# The profiles are smoothed over a window of residues: 1\n", "# The sum of all numbers in the file: 18306.4609\n", "\n", "\n", "\n", "List of the violated restraints:\n", " A restraint is violated when the relative difference\n", " from the best value (RVIOL) is larger than CUTOFF.\n", "\n", " ICSR ... index of a restraint in the current set.\n", " RESNO ... residue numbers of the first two atoms.\n", " ATM ... IUPAC atom names of the first two atoms.\n", " FEAT ... the value of the feature in the model.\n", " restr ... the mean of the basis restraint with the smallest\n", " difference from the model (local minimum).\n", " viol ... difference from the local minimum.\n", " rviol ... relative difference from the local minimum.\n", " RESTR ... the best value (global minimum).\n", " VIOL ... difference from the best value.\n", " RVIOL ... relative difference from the best value.\n", "\n", "\n", "-------------------------------------------------------------------------------------------------\n", "\n", "Feature 2 : Bond angle potential \n", "List of the RVIOL violations larger than : 4.5000\n", "\n", " # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL\n", " 1 1419 21M 21M N CA 155 156 123.55 107.00 16.55 4.76 107.00 16.55 4.76\n", "\n", "-------------------------------------------------------------------------------------------------\n", "\n", "Feature 10 : Distance restraints 2 (N-O) \n", "List of the RVIOL violations larger than : 4.5000\n", "\n", " # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL\n", " 1 7797 54S 21M N O 438 162 12.01 10.11 1.89 4.81 10.11 1.89 4.81\n", " 2 7848 56F 21M N O 448 162 7.63 5.56 2.07 5.35 5.56 2.07 5.35\n", " 3 8085 69S 89P N O 551 719 8.61 6.49 2.12 4.67 6.49 2.12 4.67\n", "\n", "-------------------------------------------------------------------------------------------------\n", "\n", "Feature 25 : Phi/Psi pair of dihedral restraints \n", "List of the RVIOL violations larger than : 6.5000\n", "\n", " # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL\n", " 1 4125 1M 2K C N 7 9 62.00 56.60 12.53 0.63 -62.90 142.25 24.85\n", " 1 2K 2K N CA 9 10 27.29 38.60 -40.80\n", " 2 4127 3V 4L C N 23 25 -101.55 -108.50 8.67 0.38 -63.50 172.76 22.11\n", " 2 4L 4L N CA 25 26 127.32 132.50 -41.20\n", " 3 4128 4L 5L C N 31 33 -113.74 -108.50 17.03 0.86 -63.50 177.36 27.72\n", " 3 5L 5L N CA 33 34 148.71 132.50 -41.20\n", " 4 4129 5L 6L C N 39 41 -59.67 -70.70 34.87 2.27 -63.50 149.77 21.02\n", " 4 6L 6L N CA 41 42 108.52 141.60 -41.20\n", " 5 4130 6L 7L C N 47 49 -136.74 -108.50 31.76 1.40 -63.50 -173.28 30.46\n", " 5 7L 7L N CA 49 50 147.04 132.50 -41.20\n", " 6 4131 7L 8G C N 55 57 -120.55 -80.20 53.21 3.83 82.20 -155.39 15.90\n", " 6 8G 8G N CA 57 58 139.41 174.10 8.50\n", " 7 4132 8G 9F C N 59 61 -123.05 -124.20 7.86 0.34 -63.20 -170.47 22.71\n", " 7 9F 9F N CA 61 62 135.53 143.30 -44.30\n", " 8 4134 10I 11F C N 78 80 -93.35 -71.40 44.11 3.92 -63.20 149.81 18.88\n", " 8 11F 11F N CA 80 81 102.44 140.70 -44.30\n", " 9 4136 12C 13S C N 95 97 -147.16 -136.60 28.25 1.17 -64.10 169.37 18.25\n", " 9 13S 13S N CA 97 98 177.39 151.20 -35.00\n", " 10 4137 13S 14M C N 101 103 -87.52 -73.00 55.55 4.01 -63.40 132.10 17.98\n", " 10 14M 14M N CA 103 104 89.38 143.00 -40.50\n", " 11 4138 14M 15A C N 109 111 179.54 -134.00 51.08 1.16 -62.50 -168.49 37.55\n", " 11 15A 15A N CA 111 112 168.23 147.00 -40.90\n", " 12 4139 15A 16A C N 114 116 -96.23 -68.20 42.27 4.15 -62.50 158.19 24.50\n", " 12 16A 16A N CA 116 117 113.66 145.30 -40.90\n", " 13 4140 16A 17H C N 119 121 -122.66 -125.60 27.42 0.98 -63.20 164.93 17.81\n", " 13 17H 17H N CA 121 122 111.54 138.80 -42.30\n", " 14 4142 18G 19K C N 133 135 -122.18 -118.00 4.56 0.21 -62.90 -172.31 21.90\n", " 14 19K 19K N CA 135 136 137.28 139.10 -40.80\n", " 15 4144 20R 21M C N 153 155 -68.70 -63.40 6.53 0.91 -73.00 179.75 12.07\n", " 15 21M 21M N CA 155 156 -36.70 -40.50 143.00\n", " 16 4145 21M 22E C N 161 163 68.75 -69.30 140.05 9.76 -69.30 140.05 9.76\n", " 16 22E 22E N CA 163 164 118.89 142.50 142.50\n", " 17 4177 53E 54S C N 436 438 -136.64 -64.10 77.51 8.57 -64.10 77.51 8.57\n", " 17 54S 54S N CA 438 439 -7.69 -35.00 -35.00\n", " 18 4188 64N 65P C N 521 523 -68.71 -64.50 67.27 4.80 -58.70 115.59 10.37\n", " 18 65P 65P N CA 523 524 -145.66 147.20 -30.50\n", " 19 4189 65P 66G C N 528 530 -52.61 -62.40 18.52 3.29 82.20 139.03 10.34\n", " 19 66G 66G N CA 530 531 -25.48 -41.20 8.50\n", " 20 4212 88T 89P C N 711 713 -43.58 -58.70 62.45 4.07 -64.50 123.49 10.35\n", " 20 89P 89P N CA 713 714 -91.10 -30.50 147.20\n", " 21 4213 89P 90H C N 718 720 -99.99 -125.60 60.30 1.76 56.30 162.20 22.66\n", " 21 90H 90H N CA 720 721 84.20 138.80 40.80\n", "\n", "-------------------------------------------------------------------------------------------------\n", "\n", "Feature 27 : Distance restraints 5 (X-Y) \n", "List of the RVIOL violations larger than : 4.5000\n", "\n", " # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL\n", " 1 13382 148. 150. C1 O1L 1180 1222 9.10 3.00 6.10 61.04 3.00 6.10 61.04\n", "\n", "\n", "report______> Distribution of short non-bonded contacts:\n", "\n", " serious non-bonded atom clash: 1180 1197 2.297\n", "\n", "DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40\n", "DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50\n", "FREQUENCY: 0 0 1 0 2 10 15 77 95 146 127 140 181 227 213\n", "\n", "\n", "<< end of ENERGY.\n", "\n", ">> Summary of successfully produced models:\n", "Filename molpdf\n", "----------------------------------------\n", "with_ligand.B99990001.pdb 2246.63257\n", "with_ligand.B99990002.pdb 2485.38550\n", "\n" ] } ], "source": [ "class mymodel(modeller.automodel.automodel):\n", " def special_restraints(self, aln):\n", " rsr = self.restraints\n", " at = self.atoms\n", " for x,y in [('C1:148','O1L:150')]:\n", " self.my_data = modeller.forms.gaussian(group=modeller.physical.xy_distance, \n", " feature=modeller.features.distance(\n", " at[x],at[y]),mean=3.0, stdev=0.1)\n", " rsr.add(modeller.forms.gaussian(group=modeller.physical.xy_distance, \n", " feature=modeller.features.distance(\n", " at[x],at[y]),mean=3.0, stdev=0.1))\n", "\n", "from modeller import *\n", "from modeller.automodel import * \n", "a = mymodel(env, alnfile='all_in_one_ligand.ali',\n", " knowns= pdb.code , sequence = alignm2[0].code)\n", "a.starting_model = 1\n", "a.ending_model = 2\n", "a.make()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Download this notebook " ] } ], "metadata": { "anaconda-cloud": {}, "kernelspec": { "display_name": "hse-py27", "language": "python", "name": "hse" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 2 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython2", "version": "2.7.3" } }, "nbformat": 4, "nbformat_minor": 1 }