B1_BrowsingConformations_Old.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "import py3Dmol\n",
    "from rdkit import Chem\n",
    "from rdkit.Chem import AllChem\n",
    "from ipywidgets import interact, interactive, fixed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "def drawit(m,p,confId=-1):\n",
    "    mb = Chem.MolToMolBlock(m,confId=confId)\n",
    "    p.removeAllModels()\n",
    "    p.addModel(mb,'sdf')\n",
    "    p.setStyle({'stick':{}})\n",
    "    p.setBackgroundColor('0xeeeeee')\n",
    "    p.zoomTo()\n",
    "    return p.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false,
    "deletable": true,
    "editable": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'2015.03.1'"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from rdkit import rdBase\n",
    "rdBase.rdkitVersion"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "deletable": true,
    "editable": true
   },
   "source": [
    "# create molecule"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "m = Chem.MolFromSmiles(r'COc1ccc2[nH]c([S@@+]([O-])Cc3ncc(C)c(OC)c3C)nc2c1') # esomeprazole\n",
    "m = Chem.AddHs(m)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "deletable": true,
    "editable": true
   },
   "source": [
    "# Generate confs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false,
    "deletable": true,
    "editable": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<rdkit.rdBase._vecti at 0x7ff59011b2d0>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "AllChem.EmbedMultipleConfs(m,numConfs=10)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "deletable": true,
    "editable": true
   },
   "source": [
    "# Align and render"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false,
    "deletable": true,
    "editable": true
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "809328b9e34846aab02a71e7a69312c6"
      }
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# align to one of the ring systems:\n",
    "AllChem.AlignMolConformers(m,m.GetSubstructMatch(Chem.MolFromSmarts('c1[nH]c2ccccc2n1')))\n",
    "\n",
    "# now construct the view and interactive widget:\n",
    "p = py3Dmol.view(width=400,height=400)\n",
    "interact(drawit, m=fixed(m),p=fixed(p),confId=(0,m.GetNumConformers()-1));\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "deletable": true,
    "editable": true
   },
   "source": [
    "Figure above: Multiple conformations"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "import sys\n",
    "import rdkit\n",
    "from rdkit import Chem\n",
    "from rdkit.Chem import AllChem\n",
    "\n",
    "SMILES = 'CCOCCn1c(C2CC[NH+](CCc3ccc(C(C)(C)C(=O)[O-])cc3)CC2)nc2ccccc21'\n",
    "HowMany = 100\n",
    "limitRMS = 2.0\n",
    "\n",
    "mol = Chem.MolFromSmiles(SMILES)\n",
    "mol = AllChem.AddHs(mol)\n",
    "allconf = AllChem.EmbedMultipleConfs(mol, numConfs = HowMany)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false,
    "deletable": true,
    "editable": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "     RDKit          \n",
      "\n",
      "  4  4  0  0  0  0  0  0  0  0999 V2000\n",
      "    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "  1  2  1  0\n",
      "  2  3  1  0\n",
      "  3  4  1  0\n",
      "  4  1  1  0\n",
      "M  END\n",
      "\n"
     ]
    }
   ],
   "source": [
    "m2 = Chem.MolFromSmiles('C1CCC1')\n",
    "print(Chem.MolToMolBlock(m2))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": [
    "m = Chem.MolFromSmiles('c1nccc2n1ccc2')\n",
    "AllChem.Compute2DCoords(m)\n",
    "template = Chem.MolFromSmiles('c1nccc2n1ccc2')\n",
    "AllChem.Compute2DCoords(template)\n",
    "AllChem.GenerateDepictionMatching2DStructure(m,template)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false,
    "deletable": true,
    "editable": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div id=\"3dmolviewer_149254592817\"  style=\"position: relative; width: 400px; height: 400px\">\n",
       "<script>\n",
       "if(typeof $3Dmolpromise === 'undefined') $3Dmolpromise = $.when($.getScript('https://3dmol.csb.pitt.edu/build/3Dmol.js'))\n",
       "var viewer_149254592817 = null;\n",
       "$3Dmolpromise.done(function() {\n",
       "viewer_149254592817 = $3Dmol.createViewer($(\"#3dmolviewer_149254592817\"),{backgroundColor:\"white\"});\n",
       "\tviewer_149254592817.addModel(\"HEADER    PLANT PROTEIN                           30-APR-81   1CRN              \\nTITLE     WATER STRUCTURE OF A HYDROPHOBIC PROTEIN AT ATOMIC RESOLUTION.        \\nTITLE    2 PENTAGON RINGS OF WATER MOLECULES IN CRYSTALS OF CRAMBIN             \\nCOMPND    MOL_ID: 1;                                                            \\nCOMPND   2 MOLECULE: CRAMBIN;                                                   \\nCOMPND   3 CHAIN: A;                                                            \\nCOMPND   4 ENGINEERED: YES                                                      \\nSOURCE    MOL_ID: 1;                                                            \\nSOURCE   2 ORGANISM_SCIENTIFIC: CRAMBE HISPANICA SUBSP. ABYSSINICA;             \\nSOURCE   3 ORGANISM_TAXID: 3721;                                                \\nSOURCE   4 STRAIN: SUBSP. ABYSSINICA                                            \\nKEYWDS    PLANT SEED PROTEIN, PLANT PROTEIN                                     \\nEXPDTA    X-RAY DIFFRACTION                                                     \\nAUTHOR    W.A.HENDRICKSON,M.M.TEETER                                            \\nREVDAT   7   11-JUL-12 1CRN    1       SCALE1 VERSN  HEADER                     \\nREVDAT   6   24-FEB-09 1CRN    1       VERSN                                    \\nREVDAT   5   16-APR-87 1CRN    1       HEADER                                   \\nREVDAT   4   04-MAR-85 1CRN    1       REMARK                                   \\nREVDAT   3   30-SEP-83 1CRN    1       REVDAT                                   \\nREVDAT   2   03-DEC-81 1CRN    1       SHEET                                    \\nREVDAT   1   28-JUL-81 1CRN    0                                                \\nJRNL        AUTH   M.M.TEETER                                                   \\nJRNL        TITL   WATER STRUCTURE OF A HYDROPHOBIC PROTEIN AT ATOMIC           \\nJRNL        TITL 2 RESOLUTION: PENTAGON RINGS OF WATER MOLECULES IN CRYSTALS OF \\nJRNL        TITL 3 CRAMBIN.                                                     \\nJRNL        REF    PROC.NATL.ACAD.SCI.USA        V.  81  6014 1984              \\nJRNL        REFN                   ISSN 0027-8424                               \\nJRNL        PMID   16593516                                                     \\nJRNL        DOI    10.1073/PNAS.81.19.6014                                      \\nREMARK   1                                                                      \\nREMARK   1 REFERENCE 1                                                          \\nREMARK   1  AUTH   W.A.HENDRICKSON,M.M.TEETER                                   \\nREMARK   1  TITL   STRUCTURE OF THE HYDROPHOBIC PROTEIN CRAMBIN DETERMINED      \\nREMARK   1  TITL 2 DIRECTLY FROM THE ANOMALOUS SCATTERING OF SULPHUR            \\nREMARK   1  REF    NATURE                        V. 290   107 1981              \\nREMARK   1  REFN                   ISSN 0028-0836                               \\nREMARK   1 REFERENCE 2                                                          \\nREMARK   1  AUTH   M.M.TEETER,W.A.HENDRICKSON                                   \\nREMARK   1  TITL   HIGHLY ORDERED CRYSTALS OF THE PLANT SEED PROTEIN CRAMBIN    \\nREMARK   1  REF    J.MOL.BIOL.                   V. 127   219 1979              \\nREMARK   1  REFN                   ISSN 0022-2836                               \\nREMARK   2                                                                      \\nREMARK   2 RESOLUTION.    1.50 ANGSTROMS.                                       \\nREMARK   3                                                                      \\nREMARK   3 REFINEMENT.                                                          \\nREMARK   3   PROGRAM     : PROLSQ                                               \\nREMARK   3   AUTHORS     : KONNERT,HENDRICKSON                                  \\nREMARK   3                                                                      \\nREMARK   3  DATA USED IN REFINEMENT.                                            \\nREMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50                           \\nREMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : NULL                           \\nREMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL                           \\nREMARK   3   COMPLETENESS FOR RANGE        (%) : NULL                           \\nREMARK   3   NUMBER OF REFLECTIONS             : NULL                           \\nREMARK   3                                                                      \\nREMARK   3  FIT TO DATA USED IN REFINEMENT.                                     \\nREMARK   3   CROSS-VALIDATION METHOD          : NULL                            \\nREMARK   3   FREE R VALUE TEST SET SELECTION  : NULL                            \\nREMARK   3   R VALUE     (WORKING + TEST SET) : NULL                            \\nREMARK   3   R VALUE            (WORKING SET) : NULL                            \\nREMARK   3   FREE R VALUE                     : NULL                            \\nREMARK   3   FREE R VALUE TEST SET SIZE   (%) : NULL                            \\nREMARK   3   FREE R VALUE TEST SET COUNT      : NULL                            \\nREMARK   3                                                                      \\nREMARK   3  FIT/AGREEMENT OF MODEL WITH ALL DATA.                               \\nREMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : NULL                   \\nREMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : NULL                   \\nREMARK   3   FREE R VALUE                  (NO CUTOFF) : NULL                   \\nREMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL                   \\nREMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : NULL                   \\nREMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : NULL                   \\nREMARK   3                                                                      \\nREMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    \\nREMARK   3   PROTEIN ATOMS            : 327                                     \\nREMARK   3   NUCLEIC ACID ATOMS       : 0                                       \\nREMARK   3   HETEROGEN ATOMS          : 0                                       \\nREMARK   3   SOLVENT ATOMS            : 0                                       \\nREMARK   3                                                                      \\nREMARK   3  B VALUES.                                                           \\nREMARK   3   FROM WILSON PLOT           (A**2) : NULL                           \\nREMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL                           \\nREMARK   3   OVERALL ANISOTROPIC B VALUE.                                       \\nREMARK   3    B11 (A**2) : NULL                                                 \\nREMARK   3    B22 (A**2) : NULL                                                 \\nREMARK   3    B33 (A**2) : NULL                                                 \\nREMARK   3    B12 (A**2) : NULL                                                 \\nREMARK   3    B13 (A**2) : NULL                                                 \\nREMARK   3    B23 (A**2) : NULL                                                 \\nREMARK   3                                                                      \\nREMARK   3  ESTIMATED COORDINATE ERROR.                                         \\nREMARK   3   ESD FROM LUZZATI PLOT        (A) : NULL                            \\nREMARK   3   ESD FROM SIGMAA              (A) : NULL                            \\nREMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL                            \\nREMARK   3                                                                      \\nREMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   \\nREMARK   3   DISTANCE RESTRAINTS.                    RMS    SIGMA               \\nREMARK   3    BOND LENGTH                     (A) : NULL  ; NULL                \\nREMARK   3    ANGLE DISTANCE                  (A) : NULL  ; NULL                \\nREMARK   3    INTRAPLANAR 1-4 DISTANCE        (A) : NULL  ; NULL                \\nREMARK   3    H-BOND OR METAL COORDINATION    (A) : NULL  ; NULL                \\nREMARK   3                                                                      \\nREMARK   3   PLANE RESTRAINT                  (A) : NULL  ; NULL                \\nREMARK   3   CHIRAL-CENTER RESTRAINT       (A**3) : NULL  ; NULL                \\nREMARK   3                                                                      \\nREMARK   3   NON-BONDED CONTACT RESTRAINTS.                                     \\nREMARK   3    SINGLE TORSION                  (A) : NULL  ; NULL                \\nREMARK   3    MULTIPLE TORSION                (A) : NULL  ; NULL                \\nREMARK   3    H-BOND (X...Y)                  (A) : NULL  ; NULL                \\nREMARK   3    H-BOND (X-H...Y)                (A) : NULL  ; NULL                \\nREMARK   3                                                                      \\nREMARK   3   CONFORMATIONAL TORSION ANGLE RESTRAINTS.                           \\nREMARK   3    SPECIFIED                 (DEGREES) : NULL  ; NULL                \\nREMARK   3    PLANAR                    (DEGREES) : NULL  ; NULL                \\nREMARK   3    STAGGERED                 (DEGREES) : NULL  ; NULL                \\nREMARK   3    TRANSVERSE                (DEGREES) : NULL  ; NULL                \\nREMARK   3                                                                      \\nREMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA                \\nREMARK   3   MAIN-CHAIN BOND               (A**2) : NULL  ; NULL                \\nREMARK   3   MAIN-CHAIN ANGLE              (A**2) : NULL  ; NULL                \\nREMARK   3   SIDE-CHAIN BOND               (A**2) : NULL  ; NULL                \\nREMARK   3   SIDE-CHAIN ANGLE              (A**2) : NULL  ; NULL                \\nREMARK   3                                                                      \\nREMARK   3  OTHER REFINEMENT REMARKS: NULL                                      \\nREMARK   4                                                                      \\nREMARK   4 1CRN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         \\nREMARK 100                                                                      \\nREMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.                                \\nREMARK 200                                                                      \\nREMARK 200 EXPERIMENTAL DETAILS                                                 \\nREMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  \\nREMARK 200  DATE OF DATA COLLECTION        : NULL                               \\nREMARK 200  TEMPERATURE           (KELVIN) : NULL                               \\nREMARK 200  PH                             : NULL                               \\nREMARK 200  NUMBER OF CRYSTALS USED        : NULL                               \\nREMARK 200                                                                      \\nREMARK 200  SYNCHROTRON              (Y/N) : NULL                               \\nREMARK 200  RADIATION SOURCE               : NULL                               \\nREMARK 200  BEAMLINE                       : NULL                               \\nREMARK 200  X-RAY GENERATOR MODEL          : NULL                               \\nREMARK 200  MONOCHROMATIC OR LAUE    (M/L) : NULL                               \\nREMARK 200  WAVELENGTH OR RANGE        (A) : NULL                               \\nREMARK 200  MONOCHROMATOR                  : NULL                               \\nREMARK 200  OPTICS                         : NULL                               \\nREMARK 200                                                                      \\nREMARK 200  DETECTOR TYPE                  : NULL                               \\nREMARK 200  DETECTOR MANUFACTURER          : NULL                               \\nREMARK 200  INTENSITY-INTEGRATION SOFTWARE : NULL                               \\nREMARK 200  DATA SCALING SOFTWARE          : NULL                               \\nREMARK 200                                                                      \\nREMARK 200  NUMBER OF UNIQUE REFLECTIONS   : NULL                               \\nREMARK 200  RESOLUTION RANGE HIGH      (A) : NULL                               \\nREMARK 200  RESOLUTION RANGE LOW       (A) : NULL                               \\nREMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               \\nREMARK 200                                                                      \\nREMARK 200 OVERALL.                                                             \\nREMARK 200  COMPLETENESS FOR RANGE     (%) : NULL                               \\nREMARK 200  DATA REDUNDANCY                : NULL                               \\nREMARK 200  R MERGE                    (I) : NULL                               \\nREMARK 200  R SYM                      (I) : NULL                               \\nREMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : NULL                               \\nREMARK 200                                                                      \\nREMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     \\nREMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL                     \\nREMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : NULL                     \\nREMARK 200  COMPLETENESS FOR SHELL     (%) : NULL                               \\nREMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               \\nREMARK 200  R MERGE FOR SHELL          (I) : NULL                               \\nREMARK 200  R SYM FOR SHELL            (I) : NULL                               \\nREMARK 200  <I/SIGMA(I)> FOR SHELL         : NULL                               \\nREMARK 200                                                                      \\nREMARK 200 DIFFRACTION PROTOCOL: NULL                                           \\nREMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL                         \\nREMARK 200 SOFTWARE USED: NULL                                                  \\nREMARK 200 STARTING MODEL: NULL                                                 \\nREMARK 200                                                                      \\nREMARK 200 REMARK: NULL                                                         \\nREMARK 280                                                                      \\nREMARK 280 CRYSTAL                                                              \\nREMARK 280 SOLVENT CONTENT, VS   (%): 32.16                                     \\nREMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81                     \\nREMARK 280                                                                      \\nREMARK 280 CRYSTALLIZATION CONDITIONS: NULL                                     \\nREMARK 290                                                                      \\nREMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            \\nREMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1                         \\nREMARK 290                                                                      \\nREMARK 290      SYMOP   SYMMETRY                                                \\nREMARK 290     NNNMMM   OPERATOR                                                \\nREMARK 290       1555   X,Y,Z                                                   \\nREMARK 290       2555   -X,Y+1/2,-Z                                             \\nREMARK 290                                                                      \\nREMARK 290     WHERE NNN -> OPERATOR NUMBER                                     \\nREMARK 290           MMM -> TRANSLATION VECTOR                                  \\nREMARK 290                                                                      \\nREMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            \\nREMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             \\nREMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                \\nREMARK 290 RELATED MOLECULES.                                                   \\nREMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            \\nREMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            \\nREMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            \\nREMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000            \\nREMARK 290   SMTRY2   2  0.000000  1.000000  0.000000        9.32500            \\nREMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000            \\nREMARK 290                                                                      \\nREMARK 290 REMARK: NULL                                                         \\nREMARK 300                                                                      \\nREMARK 300 BIOMOLECULE: 1                                                       \\nREMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                \\nREMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  \\nREMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               \\nREMARK 300 BURIED SURFACE AREA.                                                 \\nREMARK 350                                                                      \\nREMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           \\nREMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                \\nREMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          \\nREMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          \\nREMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               \\nREMARK 350                                                                      \\nREMARK 350 BIOMOLECULE: 1                                                       \\nREMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC                         \\nREMARK 350 APPLY THE FOLLOWING TO CHAINS: A                                     \\nREMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            \\nREMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            \\nREMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            \\nREMARK 400                                                                      \\nREMARK 400 COMPOUND                                                             \\nREMARK 400 THE SECONDARY STRUCTURE SPECIFICATIONS ARE THOSE DEFINED             \\nREMARK 400 IN REFERENCE 1 ABOVE AND DEPEND ON PARTICULAR DEFINITIONS            \\nREMARK 400 THAT MAY AFFECT THE DETERMINATION OF END POINTS.  PLEASE             \\nREMARK 400 CONSULT THE PRIMARY REFERENCE AND EXAMINE STRUCTURAL                 \\nREMARK 400 DETAILS SUCH AS HYDROGEN BONDING AND CONFORMATION ANGLES             \\nREMARK 400 WHEN MAKING USE OF THE SPECIFICATIONS.                               \\nREMARK 500                                                                      \\nREMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         \\nREMARK 500 SUBTOPIC: COVALENT BOND ANGLES                                       \\nREMARK 500                                                                      \\nREMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES              \\nREMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE               \\nREMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               \\nREMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                 \\nREMARK 500                                                                      \\nREMARK 500 STANDARD TABLE:                                                      \\nREMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)              \\nREMARK 500                                                                      \\nREMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999                        \\nREMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996                     \\nREMARK 500                                                                      \\nREMARK 500  M RES CSSEQI ATM1   ATM2   ATM3                                     \\nREMARK 500    ARG A  10   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.6 DEGREES          \\nREMARK 500    TYR A  29   CB  -  CG  -  CD1 ANGL. DEV. =  -4.7 DEGREES          \\nREMARK 500                                                                      \\nREMARK 500 REMARK: NULL                                                         \\nDBREF  1CRN A    1    46  UNP    P01542   CRAM_CRAAB       1     46             \\nSEQRES   1 A   46  THR THR CYS CYS PRO SER ILE VAL ALA ARG SER ASN PHE          \\nSEQRES   2 A   46  ASN VAL CYS ARG LEU PRO GLY THR PRO GLU ALA ILE CYS          \\nSEQRES   3 A   46  ALA THR TYR THR GLY CYS ILE ILE ILE PRO GLY ALA THR          \\nSEQRES   4 A   46  CYS PRO GLY ASP TYR ALA ASN                                  \\nHELIX    1  H1 ILE A    7  PRO A   19  13/10 CONFORMATION RES 17,19       13    \\nHELIX    2  H2 GLU A   23  THR A   30  1DISTORTED 3/10 AT RES 30           8    \\nSHEET    1  S1 2 THR A   1  CYS A   4  0                                        \\nSHEET    2  S1 2 CYS A  32  ILE A  35 -1                                        \\nSSBOND   1 CYS A    3    CYS A   40                          1555   1555  2.00  \\nSSBOND   2 CYS A    4    CYS A   32                          1555   1555  2.04  \\nSSBOND   3 CYS A   16    CYS A   26                          1555   1555  2.05  \\nCRYST1   40.960   18.650   22.520  90.00  90.77  90.00 P 1 21 1      2          \\nORIGX1      1.000000  0.000000  0.000000        0.00000                         \\nORIGX2      0.000000  1.000000  0.000000        0.00000                         \\nORIGX3      0.000000  0.000000  1.000000        0.00000                         \\nSCALE1      0.024414  0.000000  0.000328        0.00000                         \\nSCALE2      0.000000  0.053619  0.000000        0.00000                         \\nSCALE3      0.000000  0.000000  0.044409        0.00000                         \\nATOM      1  N   THR A   1      17.047  14.099   3.625  1.00 13.79           N  \\nATOM      2  CA  THR A   1      16.967  12.784   4.338  1.00 10.80           C  \\nATOM      3  C   THR A   1      15.685  12.755   5.133  1.00  9.19           C  \\nATOM      4  O   THR A   1      15.268  13.825   5.594  1.00  9.85           O  \\nATOM      5  CB  THR A   1      18.170  12.703   5.337  1.00 13.02           C  \\nATOM      6  OG1 THR A   1      19.334  12.829   4.463  1.00 15.06           O  \\nATOM      7  CG2 THR A   1      18.150  11.546   6.304  1.00 14.23           C  \\nATOM      8  N   THR A   2      15.115  11.555   5.265  1.00  7.81           N  \\nATOM      9  CA  THR A   2      13.856  11.469   6.066  1.00  8.31           C  \\nATOM     10  C   THR A   2      14.164  10.785   7.379  1.00  5.80           C  \\nATOM     11  O   THR A   2      14.993   9.862   7.443  1.00  6.94           O  \\nATOM     12  CB  THR A   2      12.732  10.711   5.261  1.00 10.32           C  \\nATOM     13  OG1 THR A   2      13.308   9.439   4.926  1.00 12.81           O  \\nATOM     14  CG2 THR A   2      12.484  11.442   3.895  1.00 11.90           C  \\nATOM     15  N   CYS A   3      13.488  11.241   8.417  1.00  5.24           N  \\nATOM     16  CA  CYS A   3      13.660  10.707   9.787  1.00  5.39           C  \\nATOM     17  C   CYS A   3      12.269  10.431  10.323  1.00  4.45           C  \\nATOM     18  O   CYS A   3      11.393  11.308  10.185  1.00  6.54           O  \\nATOM     19  CB  CYS A   3      14.368  11.748  10.691  1.00  5.99           C  \\nATOM     20  SG  CYS A   3      15.885  12.426  10.016  1.00  7.01           S  \\nATOM     21  N   CYS A   4      12.019   9.272  10.928  1.00  3.90           N  \\nATOM     22  CA  CYS A   4      10.646   8.991  11.408  1.00  4.24           C  \\nATOM     23  C   CYS A   4      10.654   8.793  12.919  1.00  3.72           C  \\nATOM     24  O   CYS A   4      11.659   8.296  13.491  1.00  5.30           O  \\nATOM     25  CB  CYS A   4      10.057   7.752  10.682  1.00  4.41           C  \\nATOM     26  SG  CYS A   4       9.837   8.018   8.904  1.00  4.72           S  \\nATOM     27  N   PRO A   5       9.561   9.108  13.563  1.00  3.96           N  \\nATOM     28  CA  PRO A   5       9.448   9.034  15.012  1.00  4.25           C  \\nATOM     29  C   PRO A   5       9.288   7.670  15.606  1.00  4.96           C  \\nATOM     30  O   PRO A   5       9.490   7.519  16.819  1.00  7.44           O  \\nATOM     31  CB  PRO A   5       8.230   9.957  15.345  1.00  5.11           C  \\nATOM     32  CG  PRO A   5       7.338   9.786  14.114  1.00  5.24           C  \\nATOM     33  CD  PRO A   5       8.366   9.804  12.958  1.00  5.20           C  \\nATOM     34  N   SER A   6       8.875   6.686  14.796  1.00  4.83           N  \\nATOM     35  CA  SER A   6       8.673   5.314  15.279  1.00  4.45           C  \\nATOM     36  C   SER A   6       8.753   4.376  14.083  1.00  4.99           C  \\nATOM     37  O   SER A   6       8.726   4.858  12.923  1.00  4.61           O  \\nATOM     38  CB  SER A   6       7.340   5.121  15.996  1.00  5.05           C  \\nATOM     39  OG  SER A   6       6.274   5.220  15.031  1.00  6.39           O  \\nATOM     40  N   ILE A   7       8.881   3.075  14.358  1.00  4.94           N  \\nATOM     41  CA  ILE A   7       8.912   2.083  13.258  1.00  6.33           C  \\nATOM     42  C   ILE A   7       7.581   2.090  12.506  1.00  5.32           C  \\nATOM     43  O   ILE A   7       7.670   2.031  11.245  1.00  6.85           O  \\nATOM     44  CB  ILE A   7       9.207   0.677  13.924  1.00  8.43           C  \\nATOM     45  CG1 ILE A   7      10.714   0.702  14.312  1.00  9.78           C  \\nATOM     46  CG2 ILE A   7       8.811  -0.477  12.969  1.00 11.70           C  \\nATOM     47  CD1 ILE A   7      11.185  -0.516  15.142  1.00  9.92           C  \\nATOM     48  N   VAL A   8       6.458   2.162  13.159  1.00  5.02           N  \\nATOM     49  CA  VAL A   8       5.145   2.209  12.453  1.00  6.93           C  \\nATOM     50  C   VAL A   8       5.115   3.379  11.461  1.00  5.39           C  \\nATOM     51  O   VAL A   8       4.664   3.268  10.343  1.00  6.30           O  \\nATOM     52  CB  VAL A   8       3.995   2.354  13.478  1.00  9.64           C  \\nATOM     53  CG1 VAL A   8       2.716   2.891  12.869  1.00 13.85           C  \\nATOM     54  CG2 VAL A   8       3.758   1.032  14.208  1.00 11.97           C  \\nATOM     55  N   ALA A   9       5.606   4.546  11.941  1.00  3.73           N  \\nATOM     56  CA  ALA A   9       5.598   5.767  11.082  1.00  3.56           C  \\nATOM     57  C   ALA A   9       6.441   5.527   9.850  1.00  4.13           C  \\nATOM     58  O   ALA A   9       6.052   5.933   8.744  1.00  4.36           O  \\nATOM     59  CB  ALA A   9       6.022   6.977  11.891  1.00  4.80           C  \\nATOM     60  N   ARG A  10       7.647   4.909  10.005  1.00  3.73           N  \\nATOM     61  CA  ARG A  10       8.496   4.609   8.837  1.00  3.38           C  \\nATOM     62  C   ARG A  10       7.798   3.609   7.876  1.00  3.47           C  \\nATOM     63  O   ARG A  10       7.878   3.778   6.651  1.00  4.67           O  \\nATOM     64  CB  ARG A  10       9.847   4.020   9.305  1.00  3.95           C  \\nATOM     65  CG  ARG A  10      10.752   3.607   8.149  1.00  4.55           C  \\nATOM     66  CD  ARG A  10      11.226   4.699   7.244  1.00  5.89           C  \\nATOM     67  NE  ARG A  10      12.143   5.571   8.035  1.00  6.20           N  \\nATOM     68  CZ  ARG A  10      12.758   6.609   7.443  1.00  7.52           C  \\nATOM     69  NH1 ARG A  10      12.539   6.932   6.158  1.00 10.68           N  \\nATOM     70  NH2 ARG A  10      13.601   7.322   8.202  1.00  9.48           N  \\nATOM     71  N   SER A  11       7.186   2.582   8.445  1.00  5.19           N  \\nATOM     72  CA  SER A  11       6.500   1.584   7.565  1.00  4.60           C  \\nATOM     73  C   SER A  11       5.382   2.313   6.773  1.00  4.84           C  \\nATOM     74  O   SER A  11       5.213   2.016   5.557  1.00  5.84           O  \\nATOM     75  CB  SER A  11       5.908   0.462   8.400  1.00  5.91           C  \\nATOM     76  OG  SER A  11       6.990  -0.272   9.012  1.00  8.38           O  \\nATOM     77  N   ASN A  12       4.648   3.182   7.446  1.00  3.54           N  \\nATOM     78  CA  ASN A  12       3.545   3.935   6.751  1.00  4.57           C  \\nATOM     79  C   ASN A  12       4.107   4.851   5.691  1.00  4.14           C  \\nATOM     80  O   ASN A  12       3.536   5.001   4.617  1.00  5.52           O  \\nATOM     81  CB  ASN A  12       2.663   4.677   7.748  1.00  6.42           C  \\nATOM     82  CG  ASN A  12       1.802   3.735   8.610  1.00  8.25           C  \\nATOM     83  OD1 ASN A  12       1.567   2.613   8.165  1.00 12.72           O  \\nATOM     84  ND2 ASN A  12       1.394   4.252   9.767  1.00  9.92           N  \\nATOM     85  N   PHE A  13       5.259   5.498   6.005  1.00  3.43           N  \\nATOM     86  CA  PHE A  13       5.929   6.358   5.055  1.00  3.49           C  \\nATOM     87  C   PHE A  13       6.304   5.578   3.799  1.00  3.40           C  \\nATOM     88  O   PHE A  13       6.136   6.072   2.653  1.00  4.07           O  \\nATOM     89  CB  PHE A  13       7.183   6.994   5.754  1.00  5.48           C  \\nATOM     90  CG  PHE A  13       7.884   8.006   4.883  1.00  5.57           C  \\nATOM     91  CD1 PHE A  13       8.906   7.586   4.027  1.00  6.99           C  \\nATOM     92  CD2 PHE A  13       7.532   9.373   4.983  1.00  6.52           C  \\nATOM     93  CE1 PHE A  13       9.560   8.539   3.194  1.00  8.20           C  \\nATOM     94  CE2 PHE A  13       8.176  10.281   4.145  1.00  6.34           C  \\nATOM     95  CZ  PHE A  13       9.141   9.845   3.292  1.00  6.84           C  \\nATOM     96  N   ASN A  14       6.900   4.390   3.989  1.00  3.64           N  \\nATOM     97  CA  ASN A  14       7.331   3.607   2.791  1.00  4.31           C  \\nATOM     98  C   ASN A  14       6.116   3.210   1.915  1.00  3.98           C  \\nATOM     99  O   ASN A  14       6.240   3.144   0.684  1.00  6.22           O  \\nATOM    100  CB  ASN A  14       8.145   2.404   3.240  1.00  5.81           C  \\nATOM    101  CG  ASN A  14       9.555   2.856   3.730  1.00  6.82           C  \\nATOM    102  OD1 ASN A  14      10.013   3.895   3.323  1.00  9.43           O  \\nATOM    103  ND2 ASN A  14      10.120   1.956   4.539  1.00  8.21           N  \\nATOM    104  N   VAL A  15       4.993   2.927   2.571  1.00  3.76           N  \\nATOM    105  CA  VAL A  15       3.782   2.599   1.742  1.00  3.98           C  \\nATOM    106  C   VAL A  15       3.296   3.871   1.004  1.00  3.80           C  \\nATOM    107  O   VAL A  15       2.947   3.817  -0.189  1.00  4.85           O  \\nATOM    108  CB  VAL A  15       2.698   1.953   2.608  1.00  4.71           C  \\nATOM    109  CG1 VAL A  15       1.384   1.826   1.806  1.00  6.67           C  \\nATOM    110  CG2 VAL A  15       3.174   0.533   3.005  1.00  6.26           C  \\nATOM    111  N   CYS A  16       3.321   4.987   1.720  1.00  3.79           N  \\nATOM    112  CA  CYS A  16       2.890   6.285   1.126  1.00  3.54           C  \\nATOM    113  C   CYS A  16       3.687   6.597  -0.111  1.00  3.48           C  \\nATOM    114  O   CYS A  16       3.200   7.147  -1.103  1.00  4.63           O  \\nATOM    115  CB  CYS A  16       3.039   7.369   2.240  1.00  4.58           C  \\nATOM    116  SG  CYS A  16       2.559   9.014   1.649  1.00  5.66           S  \\nATOM    117  N   ARG A  17       4.997   6.227  -0.100  1.00  3.99           N  \\nATOM    118  CA  ARG A  17       5.895   6.489  -1.213  1.00  3.83           C  \\nATOM    119  C   ARG A  17       5.738   5.560  -2.409  1.00  3.79           C  \\nATOM    120  O   ARG A  17       6.228   5.901  -3.507  1.00  5.39           O  \\nATOM    121  CB  ARG A  17       7.370   6.507  -0.731  1.00  4.11           C  \\nATOM    122  CG  ARG A  17       7.717   7.687   0.206  1.00  4.69           C  \\nATOM    123  CD  ARG A  17       7.949   8.947  -0.615  1.00  5.10           C  \\nATOM    124  NE  ARG A  17       9.212   8.856  -1.337  1.00  4.71           N  \\nATOM    125  CZ  ARG A  17       9.537   9.533  -2.431  1.00  5.28           C  \\nATOM    126  NH1 ARG A  17       8.659  10.350  -3.032  1.00  6.67           N  \\nATOM    127  NH2 ARG A  17      10.793   9.491  -2.899  1.00  6.41           N  \\nATOM    128  N   LEU A  18       5.051   4.411  -2.204  1.00  4.70           N  \\nATOM    129  CA  LEU A  18       4.933   3.431  -3.326  1.00  5.46           C  \\nATOM    130  C   LEU A  18       4.397   4.014  -4.620  1.00  5.13           C  \\nATOM    131  O   LEU A  18       4.988   3.755  -5.687  1.00  5.55           O  \\nATOM    132  CB  LEU A  18       4.196   2.184  -2.863  1.00  6.47           C  \\nATOM    133  CG  LEU A  18       4.960   1.178  -1.991  1.00  7.43           C  \\nATOM    134  CD1 LEU A  18       3.907   0.097  -1.634  1.00  8.70           C  \\nATOM    135  CD2 LEU A  18       6.129   0.606  -2.768  1.00  9.39           C  \\nATOM    136  N   PRO A  19       3.329   4.795  -4.543  1.00  4.28           N  \\nATOM    137  CA  PRO A  19       2.792   5.376  -5.797  1.00  5.38           C  \\nATOM    138  C   PRO A  19       3.573   6.540  -6.322  1.00  6.30           C  \\nATOM    139  O   PRO A  19       3.260   7.045  -7.422  1.00  9.62           O  \\nATOM    140  CB  PRO A  19       1.358   5.766  -5.472  1.00  5.87           C  \\nATOM    141  CG  PRO A  19       1.223   5.694  -3.993  1.00  6.47           C  \\nATOM    142  CD  PRO A  19       2.421   4.941  -3.408  1.00  6.45           C  \\nATOM    143  N   GLY A  20       4.565   7.047  -5.559  1.00  4.94           N  \\nATOM    144  CA  GLY A  20       5.366   8.191  -6.018  1.00  5.39           C  \\nATOM    145  C   GLY A  20       5.007   9.481  -5.280  1.00  5.03           C  \\nATOM    146  O   GLY A  20       5.535  10.510  -5.730  1.00  7.34           O  \\nATOM    147  N   THR A  21       4.181   9.438  -4.262  1.00  4.10           N  \\nATOM    148  CA  THR A  21       3.767  10.609  -3.513  1.00  3.94           C  \\nATOM    149  C   THR A  21       5.017  11.397  -3.042  1.00  3.96           C  \\nATOM    150  O   THR A  21       5.947  10.757  -2.523  1.00  5.82           O  \\nATOM    151  CB  THR A  21       2.992  10.188  -2.225  1.00  4.13           C  \\nATOM    152  OG1 THR A  21       2.051   9.144  -2.623  1.00  5.45           O  \\nATOM    153  CG2 THR A  21       2.260  11.349  -1.551  1.00  5.41           C  \\nATOM    154  N   PRO A  22       4.971  12.703  -3.176  1.00  5.04           N  \\nATOM    155  CA  PRO A  22       6.143  13.513  -2.696  1.00  4.69           C  \\nATOM    156  C   PRO A  22       6.400  13.233  -1.225  1.00  4.19           C  \\nATOM    157  O   PRO A  22       5.485  13.061  -0.382  1.00  4.47           O  \\nATOM    158  CB  PRO A  22       5.703  14.969  -2.920  1.00  7.12           C  \\nATOM    159  CG  PRO A  22       4.676  14.893  -3.996  1.00  7.03           C  \\nATOM    160  CD  PRO A  22       3.964  13.567  -3.811  1.00  4.90           C  \\nATOM    161  N   GLU A  23       7.728  13.297  -0.921  1.00  5.16           N  \\nATOM    162  CA  GLU A  23       8.114  13.103   0.500  1.00  5.31           C  \\nATOM    163  C   GLU A  23       7.427  14.073   1.410  1.00  4.11           C  \\nATOM    164  O   GLU A  23       7.036  13.682   2.540  1.00  5.11           O  \\nATOM    165  CB  GLU A  23       9.648  13.285   0.660  1.00  6.16           C  \\nATOM    166  CG  GLU A  23      10.440  12.093   0.063  1.00  7.48           C  \\nATOM    167  CD  GLU A  23      11.941  12.170   0.391  1.00  9.40           C  \\nATOM    168  OE1 GLU A  23      12.416  13.225   0.681  1.00 10.40           O  \\nATOM    169  OE2 GLU A  23      12.539  11.070   0.292  1.00 13.32           O  \\nATOM    170  N   ALA A  24       7.212  15.334   0.966  1.00  4.56           N  \\nATOM    171  CA  ALA A  24       6.614  16.317   1.913  1.00  4.49           C  \\nATOM    172  C   ALA A  24       5.212  15.936   2.350  1.00  4.10           C  \\nATOM    173  O   ALA A  24       4.782  16.166   3.495  1.00  5.64           O  \\nATOM    174  CB  ALA A  24       6.605  17.695   1.246  1.00  5.80           C  \\nATOM    175  N   ILE A  25       4.445  15.318   1.405  1.00  4.37           N  \\nATOM    176  CA  ILE A  25       3.074  14.894   1.756  1.00  5.44           C  \\nATOM    177  C   ILE A  25       3.085  13.643   2.645  1.00  4.32           C  \\nATOM    178  O   ILE A  25       2.315  13.523   3.578  1.00  4.72           O  \\nATOM    179  CB  ILE A  25       2.204  14.637   0.462  1.00  6.42           C  \\nATOM    180  CG1 ILE A  25       1.815  16.048  -0.129  1.00  7.50           C  \\nATOM    181  CG2 ILE A  25       0.903  13.864   0.811  1.00  7.65           C  \\nATOM    182  CD1 ILE A  25       0.756  16.761   0.757  1.00  7.80           C  \\nATOM    183  N   CYS A  26       4.032  12.764   2.313  1.00  3.92           N  \\nATOM    184  CA  CYS A  26       4.180  11.549   3.187  1.00  4.37           C  \\nATOM    185  C   CYS A  26       4.632  11.944   4.596  1.00  3.95           C  \\nATOM    186  O   CYS A  26       4.227  11.252   5.547  1.00  4.74           O  \\nATOM    187  CB  CYS A  26       5.038  10.518   2.539  1.00  4.63           C  \\nATOM    188  SG  CYS A  26       4.349   9.794   1.022  1.00  5.61           S  \\nATOM    189  N   ALA A  27       5.408  13.012   4.694  1.00  3.89           N  \\nATOM    190  CA  ALA A  27       5.879  13.502   6.026  1.00  4.43           C  \\nATOM    191  C   ALA A  27       4.696  13.908   6.882  1.00  4.26           C  \\nATOM    192  O   ALA A  27       4.528  13.422   8.025  1.00  5.44           O  \\nATOM    193  CB  ALA A  27       6.880  14.615   5.830  1.00  5.36           C  \\nATOM    194  N   THR A  28       3.827  14.802   6.358  1.00  4.53           N  \\nATOM    195  CA  THR A  28       2.691  15.221   7.194  1.00  5.08           C  \\nATOM    196  C   THR A  28       1.672  14.132   7.434  1.00  4.62           C  \\nATOM    197  O   THR A  28       0.947  14.112   8.468  1.00  7.80           O  \\nATOM    198  CB  THR A  28       1.986  16.520   6.614  1.00  6.03           C  \\nATOM    199  OG1 THR A  28       1.664  16.221   5.230  1.00  7.19           O  \\nATOM    200  CG2 THR A  28       2.914  17.739   6.700  1.00  7.34           C  \\nATOM    201  N   TYR A  29       1.621  13.190   6.511  1.00  5.01           N  \\nATOM    202  CA  TYR A  29       0.715  12.045   6.657  1.00  6.60           C  \\nATOM    203  C   TYR A  29       1.125  11.125   7.815  1.00  4.92           C  \\nATOM    204  O   TYR A  29       0.286  10.632   8.545  1.00  7.13           O  \\nATOM    205  CB  TYR A  29       0.755  11.229   5.322  1.00  9.66           C  \\nATOM    206  CG  TYR A  29      -0.203  10.044   5.354  1.00 11.56           C  \\nATOM    207  CD1 TYR A  29      -1.547  10.337   5.645  1.00 12.85           C  \\nATOM    208  CD2 TYR A  29       0.193   8.750   5.100  1.00 14.44           C  \\nATOM    209  CE1 TYR A  29      -2.496   9.329   5.673  1.00 16.61           C  \\nATOM    210  CE2 TYR A  29      -0.801   7.705   5.156  1.00 17.11           C  \\nATOM    211  CZ  TYR A  29      -2.079   8.031   5.430  1.00 19.99           C  \\nATOM    212  OH  TYR A  29      -3.097   7.057   5.458  1.00 28.98           O  \\nATOM    213  N   THR A  30       2.470  10.984   7.995  1.00  5.31           N  \\nATOM    214  CA  THR A  30       2.986   9.994   8.950  1.00  5.70           C  \\nATOM    215  C   THR A  30       3.609  10.505  10.230  1.00  6.28           C  \\nATOM    216  O   THR A  30       3.766   9.715  11.186  1.00  8.77           O  \\nATOM    217  CB  THR A  30       4.076   9.103   8.225  1.00  6.55           C  \\nATOM    218  OG1 THR A  30       5.125  10.027   7.824  1.00  6.57           O  \\nATOM    219  CG2 THR A  30       3.493   8.324   7.035  1.00  7.29           C  \\nATOM    220  N   GLY A  31       3.984  11.764  10.241  1.00  4.99           N  \\nATOM    221  CA  GLY A  31       4.769  12.336  11.360  1.00  5.50           C  \\nATOM    222  C   GLY A  31       6.255  12.243  11.106  1.00  4.19           C  \\nATOM    223  O   GLY A  31       7.037  12.750  11.954  1.00  6.12           O  \\nATOM    224  N   CYS A  32       6.710  11.631   9.992  1.00  4.30           N  \\nATOM    225  CA  CYS A  32       8.140  11.694   9.635  1.00  4.89           C  \\nATOM    226  C   CYS A  32       8.500  13.141   9.206  1.00  5.50           C  \\nATOM    227  O   CYS A  32       7.581  13.949   8.944  1.00  5.82           O  \\nATOM    228  CB  CYS A  32       8.504  10.686   8.530  1.00  4.66           C  \\nATOM    229  SG  CYS A  32       8.048   8.987   8.881  1.00  5.33           S  \\nATOM    230  N   ILE A  33       9.793  13.410   9.173  1.00  6.02           N  \\nATOM    231  CA  ILE A  33      10.280  14.760   8.823  1.00  5.24           C  \\nATOM    232  C   ILE A  33      11.346  14.658   7.743  1.00  5.16           C  \\nATOM    233  O   ILE A  33      11.971  13.583   7.552  1.00  7.19           O  \\nATOM    234  CB  ILE A  33      10.790  15.535  10.085  1.00  5.49           C  \\nATOM    235  CG1 ILE A  33      12.059  14.803  10.671  1.00  6.85           C  \\nATOM    236  CG2 ILE A  33       9.684  15.686  11.138  1.00  6.45           C  \\nATOM    237  CD1 ILE A  33      12.733  15.676  11.781  1.00  8.94           C  \\nATOM    238  N   ILE A  34      11.490  15.773   7.038  1.00  5.52           N  \\nATOM    239  CA  ILE A  34      12.552  15.877   6.036  1.00  6.82           C  \\nATOM    240  C   ILE A  34      13.590  16.917   6.560  1.00  6.92           C  \\nATOM    241  O   ILE A  34      13.168  18.006   6.945  1.00  9.22           O  \\nATOM    242  CB  ILE A  34      11.987  16.360   4.681  1.00  8.11           C  \\nATOM    243  CG1 ILE A  34      10.914  15.338   4.163  1.00  9.59           C  \\nATOM    244  CG2 ILE A  34      13.131  16.517   3.629  1.00  9.73           C  \\nATOM    245  CD1 ILE A  34      10.151  16.024   2.938  1.00 13.41           C  \\nATOM    246  N   ILE A  35      14.856  16.493   6.536  1.00  7.06           N  \\nATOM    247  CA  ILE A  35      15.930  17.454   6.941  1.00  7.52           C  \\nATOM    248  C   ILE A  35      16.913  17.550   5.819  1.00  6.63           C  \\nATOM    249  O   ILE A  35      17.097  16.660   4.970  1.00  7.90           O  \\nATOM    250  CB  ILE A  35      16.622  16.995   8.285  1.00  8.07           C  \\nATOM    251  CG1 ILE A  35      17.360  15.651   8.067  1.00  9.41           C  \\nATOM    252  CG2 ILE A  35      15.592  16.974   9.434  1.00  9.46           C  \\nATOM    253  CD1 ILE A  35      18.298  15.206   9.219  1.00  9.85           C  \\nATOM    254  N   PRO A  36      17.664  18.669   5.806  1.00  8.07           N  \\nATOM    255  CA  PRO A  36      18.635  18.861   4.738  1.00  8.78           C  \\nATOM    256  C   PRO A  36      19.925  18.042   4.949  1.00  8.31           C  \\nATOM    257  O   PRO A  36      20.593  17.742   3.945  1.00  9.09           O  \\nATOM    258  CB  PRO A  36      18.945  20.364   4.783  1.00  9.67           C  \\nATOM    259  CG  PRO A  36      18.238  20.937   5.908  1.00 10.15           C  \\nATOM    260  CD  PRO A  36      17.371  19.900   6.596  1.00  9.53           C  \\nATOM    261  N   GLY A  37      20.172  17.730   6.217  1.00  8.48           N  \\nATOM    262  CA  GLY A  37      21.452  16.969   6.513  1.00  9.20           C  \\nATOM    263  C   GLY A  37      21.143  15.478   6.427  1.00 10.41           C  \\nATOM    264  O   GLY A  37      20.138  15.023   5.878  1.00 12.06           O  \\nATOM    265  N   ALA A  38      22.055  14.701   7.032  1.00  9.24           N  \\nATOM    266  CA  ALA A  38      22.019  13.242   7.020  1.00  9.24           C  \\nATOM    267  C   ALA A  38      21.944  12.628   8.396  1.00  9.60           C  \\nATOM    268  O   ALA A  38      21.869  11.387   8.435  1.00 13.65           O  \\nATOM    269  CB  ALA A  38      23.246  12.697   6.275  1.00 10.43           C  \\nATOM    270  N   THR A  39      21.894  13.435   9.436  1.00  8.70           N  \\nATOM    271  CA  THR A  39      21.936  12.911  10.809  1.00  9.46           C  \\nATOM    272  C   THR A  39      20.615  13.191  11.521  1.00  8.32           C  \\nATOM    273  O   THR A  39      20.357  14.317  11.948  1.00  9.89           O  \\nATOM    274  CB  THR A  39      23.131  13.601  11.593  1.00 10.72           C  \\nATOM    275  OG1 THR A  39      24.284  13.401  10.709  1.00 11.66           O  \\nATOM    276  CG2 THR A  39      23.340  12.935  12.962  1.00 11.81           C  \\nATOM    277  N   CYS A  40      19.827  12.110  11.642  1.00  7.64           N  \\nATOM    278  CA  CYS A  40      18.504  12.312  12.298  1.00  8.05           C  \\nATOM    279  C   CYS A  40      18.684  12.451  13.784  1.00  7.63           C  \\nATOM    280  O   CYS A  40      19.533  11.718  14.362  1.00  9.64           O  \\nATOM    281  CB  CYS A  40      17.582  11.117  11.996  1.00  7.80           C  \\nATOM    282  SG  CYS A  40      17.199  10.929  10.237  1.00  7.30           S  \\nATOM    283  N   PRO A  41      17.880  13.266  14.426  1.00  8.00           N  \\nATOM    284  CA  PRO A  41      17.924  13.421  15.877  1.00  8.96           C  \\nATOM    285  C   PRO A  41      17.392  12.206  16.594  1.00  9.06           C  \\nATOM    286  O   PRO A  41      16.652  11.368  16.033  1.00  8.82           O  \\nATOM    287  CB  PRO A  41      17.076  14.658  16.145  1.00 10.39           C  \\nATOM    288  CG  PRO A  41      16.098  14.689  14.997  1.00 10.99           C  \\nATOM    289  CD  PRO A  41      16.859  14.150  13.779  1.00 10.49           C  \\nATOM    290  N   GLY A  42      17.728  12.124  17.884  1.00  7.55           N  \\nATOM    291  CA  GLY A  42      17.334  10.956  18.691  1.00  8.00           C  \\nATOM    292  C   GLY A  42      15.875  10.688  18.871  1.00  7.22           C  \\nATOM    293  O   GLY A  42      15.434   9.550  19.166  1.00  8.41           O  \\nATOM    294  N   ASP A  43      15.036  11.747  18.715  1.00  5.54           N  \\nATOM    295  CA  ASP A  43      13.564  11.573  18.836  1.00  5.85           C  \\nATOM    296  C   ASP A  43      12.936  11.227  17.470  1.00  5.87           C  \\nATOM    297  O   ASP A  43      11.720  11.040  17.428  1.00  7.29           O  \\nATOM    298  CB  ASP A  43      12.933  12.737  19.580  1.00  6.72           C  \\nATOM    299  CG  ASP A  43      13.140  14.094  18.958  1.00  8.59           C  \\nATOM    300  OD1 ASP A  43      14.109  14.303  18.212  1.00  9.59           O  \\nATOM    301  OD2 ASP A  43      12.267  14.963  19.265  1.00 11.45           O  \\nATOM    302  N   TYR A  44      13.725  11.174  16.425  1.00  5.22           N  \\nATOM    303  CA  TYR A  44      13.257  10.745  15.081  1.00  5.56           C  \\nATOM    304  C   TYR A  44      14.275   9.687  14.612  1.00  4.61           C  \\nATOM    305  O   TYR A  44      14.930   9.862  13.568  1.00  6.04           O  \\nATOM    306  CB  TYR A  44      13.200  11.914  14.071  1.00  5.41           C  \\nATOM    307  CG  TYR A  44      12.000  12.819  14.399  1.00  5.34           C  \\nATOM    308  CD1 TYR A  44      12.119  13.853  15.332  1.00  6.59           C  \\nATOM    309  CD2 TYR A  44      10.775  12.617  13.762  1.00  5.94           C  \\nATOM    310  CE1 TYR A  44      11.045  14.675  15.610  1.00  5.97           C  \\nATOM    311  CE2 TYR A  44       9.676  13.433  14.048  1.00  5.17           C  \\nATOM    312  CZ  TYR A  44       9.802  14.456  14.996  1.00  5.96           C  \\nATOM    313  OH  TYR A  44       8.740  15.265  15.269  1.00  8.60           O  \\nATOM    314  N   ALA A  45      14.342   8.640  15.422  1.00  4.76           N  \\nATOM    315  CA  ALA A  45      15.445   7.667  15.246  1.00  5.89           C  \\nATOM    316  C   ALA A  45      15.171   6.533  14.280  1.00  6.67           C  \\nATOM    317  O   ALA A  45      16.093   5.705  14.039  1.00  7.56           O  \\nATOM    318  CB  ALA A  45      15.680   7.099  16.682  1.00  6.82           C  \\nATOM    319  N   ASN A  46      13.966   6.502  13.739  1.00  5.80           N  \\nATOM    320  CA  ASN A  46      13.512   5.395  12.878  1.00  6.15           C  \\nATOM    321  C   ASN A  46      13.311   5.853  11.455  1.00  6.61           C  \\nATOM    322  O   ASN A  46      13.733   6.929  11.026  1.00  7.18           O  \\nATOM    323  CB  ASN A  46      12.266   4.769  13.501  1.00  7.27           C  \\nATOM    324  CG  ASN A  46      12.538   4.304  14.922  1.00  7.98           C  \\nATOM    325  OD1 ASN A  46      11.982   4.849  15.886  1.00 11.00           O  \\nATOM    326  ND2 ASN A  46      13.407   3.298  15.015  1.00 10.32           N  \\nATOM    327  OXT ASN A  46      12.703   4.973  10.746  1.00  7.86           O  \\nTER     328      ASN A  46                                                      \\nCONECT   20  282                                                                \\nCONECT   26  229                                                                \\nCONECT  116  188                                                                \\nCONECT  188  116                                                                \\nCONECT  229   26                                                                \\nCONECT  282   20                                                                \\nMASTER      224    0    0    2    2    1    0    6  327    1    6    4          \\nEND                                                                             \\n\",\"pdb\");\n",
       "\tviewer_149254592817.setStyle({\"stick\": {}});\n",
       "\tviewer_149254592817.setBackgroundColor(\"0xeeeeee\");\n",
       "\tviewer_149254592817.zoomTo();\n",
       "viewer_149254592817.render();\n",
       "});\n",
       "</script>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "crambin = open('1CRN.pdb','r').read()\n",
    "p = py3Dmol.view(width=400,height=400)\n",
    "p.addModel(crambin,'pdb')\n",
    "p.setStyle({'stick':{}})\n",
    "p.setBackgroundColor('0xeeeeee')\n",
    "p.zoomTo()\n",
    "p.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false,
    "deletable": true,
    "editable": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/usr/local/lib/python2.7/dist-packages/py3Dmol/__init__.pyc'"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import inspect\n",
    "inspect.getfile(py3Dmol)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true,
    "deletable": true,
    "editable": true
   },
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
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    "version": 2
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   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
   "version": "2.7.12"
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  "widgets": {
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    "cd43f35def31486eaae5a1f6cb75ca50": {
     "views": [
      {
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    "daea107d35ae40fe8a42d54c61a850e7": {
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 },
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