reconstruct-beranek.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "05fd1ae1-4ce1-4e2d-bfc2-e7daeb3699c3",
   "metadata": {},
   "outputs": [],
   "source": [
    "import gromacs as gmx\n",
    "from gromacs import formats as gmf\n",
    "import numpy as np\n",
    "import mdtraj as md\n",
    "import nglview as nv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "5893fc87-3f53-4fe7-bc74-6ff6556c1415",
   "metadata": {},
   "outputs": [],
   "source": [
    "dir='/home/meta/ljocha/ASMSA/My_AE/trpcage/ae'\n",
    "ftrain=dir + '/trpcage_ds.npy'\n",
    "pdb = dir + '/trpcage_npt400.pdb'\n",
    "xtc = dir + '/trpcage_ds_fit.xtc'\n",
    "dec = '/home/meta/ljocha/ASMSA/My_AE/trpcage/dec_out_LS_matrix_pos_32x32.npy'\n",
    "\n",
    "train = np.load(ftrain)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "3e04828a-2ca1-47c5-a522-25f600929429",
   "metadata": {},
   "outputs": [],
   "source": [
    "train_view = np.reshape(train,(-1,272,3))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "df25389f-2c70-48dd-b64b-bda035c58f61",
   "metadata": {},
   "outputs": [],
   "source": [
    "train.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "117c6c9b-5a3b-49f4-a86b-9a0c913495de",
   "metadata": {},
   "outputs": [],
   "source": [
    "tr = md.load(pdb)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "3552af34-90b8-46ea-bebd-aeb303cbe73b",
   "metadata": {},
   "outputs": [],
   "source": [
    "tr.xyz = train_view"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "82556e98-b764-4b43-92cf-edeff3bfb09b",
   "metadata": {},
   "outputs": [],
   "source": [
    "v=nv.show_mdtraj(tr)\n",
    "v"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "1ed1c87d-8edd-4a31-a2c8-2d7f7a65c8b9",
   "metadata": {},
   "outputs": [],
   "source": [
    "dec_out_all = np.load(dec)\n",
    "dec_out_all.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ab4c3c38-3bfc-4494-a731-47d5d3bb7626",
   "metadata": {},
   "outputs": [],
   "source": [
    "def Unstandardize(x):\n",
    "    x = np.array(x)\n",
    "    return ((x*7)-1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f79feefd-48b4-46e7-98d8-5dc73b243a5a",
   "metadata": {},
   "outputs": [],
   "source": [
    "dec_out_all = Unstandardize(dec_out_all)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "028a98ff-287d-4b5a-899b-3ae45af5498b",
   "metadata": {},
   "outputs": [],
   "source": [
    "dec_out = dec_out_all[6,18]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "a8e04d29-6fd5-4bc3-8575-52e7dff55ada",
   "metadata": {},
   "outputs": [],
   "source": [
    "diff = train - dec_out\n",
    "msd = np.sum(diff * diff,axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "49a3a810-5ea4-43f0-b792-1ecf1aa8cfe1",
   "metadata": {},
   "outputs": [],
   "source": [
    "imin = np.argmin(msd)\n",
    "imin"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c5767e9c-b461-4e30-92bd-6ba9e749cc79",
   "metadata": {},
   "outputs": [],
   "source": [
    "tr2 = md.load(pdb)\n",
    "tr2.xyz = np.reshape(dec_out_all,(-1,272,3))\n",
    "#tr2.xyz = train_view[9873]\n",
    "v2 = nv.show_mdtraj(tr2)\n",
    "#v2.clear()\n",
    "v2.add_representation(\"licorice\")\n",
    "v2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "dd92021c-c032-45a3-b41b-7559e7125bd6",
   "metadata": {},
   "outputs": [],
   "source": [
    "v.frame=int(imin)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "07e2429d-758e-4ae4-abeb-40679ccbacec",
   "metadata": {},
   "outputs": [],
   "source": [
    "tr3 = md.load(xtc,top=pdb)\n",
    "tr3.xyz = np.reshape(dec_out_all,(-1,272,3))\n",
    "tr3.time = tr3.time[0:tr3.xyz.shape[0]]\n",
    "tr3.unitcell_vectors = tr3.unitcell_vectors[0:tr3.xyz.shape[0]]\n",
    "\n",
    "tr3.save_xtc('simulated.xtc')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0e1296d9-f2d9-4b49-85d3-6f09b4c92253",
   "metadata": {},
   "source": [
    "### Identify backbone atoms"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "93879b44-6947-477d-8bae-ff8504c23569",
   "metadata": {},
   "outputs": [],
   "source": [
    "!cp {pdb} reference.pdb"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "7782b57e-231c-441f-aff1-e0f57b3d1ac6",
   "metadata": {},
   "outputs": [],
   "source": [
    "gmx.select(s='reference.pdb',on='bb.ndx',select='Backbone')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "9e2e5146-10d7-4595-a34b-fe559b064c5a",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "2dc8770c-bb0f-4bf3-94aa-64cffbdd7e35",
   "metadata": {},
   "source": [
    "### Compute backbone dihedrals of the simulated trajectory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "31160b0c-7d61-4bbf-8043-05c5159bb360",
   "metadata": {},
   "outputs": [],
   "source": [
    "with open('bb.ndx') as bb:\n",
    "    bb.readline()\n",
    "    l = \" \".join(bb.readlines())\n",
    "    ndx = np.array(l.split(),np.int32)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6584b8f7-9a7f-43a1-a7a5-1565e7499b1e",
   "metadata": {},
   "outputs": [],
   "source": [
    "with open('angle.ndx','w') as a:\n",
    "    a.write('[ dihedrals ]\\n')\n",
    "    for i in range(0,len(ndx)-3):\n",
    "        a.write('  '.join(map(str,ndx[i:i+4])))\n",
    "        a.write('\\n')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e0c211ab-4086-40b3-96db-f3303263a7c7",
   "metadata": {},
   "outputs": [],
   "source": [
    "gmx.gangle(f='simulated.xtc',n='angle.ndx',g1='dihedral',group1='dihedrals',oall='dihedrals.xvg')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "92f03615-615d-4576-962c-83e64b0572a1",
   "metadata": {},
   "outputs": [],
   "source": [
    "dihs = gmf.XVG('dihedrals.xvg').array[1:]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c4730dba-a646-4edf-bcb9-c25054a9357c",
   "metadata": {},
   "source": [
    "### Generate restrained topology and run minimization"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "fecfd064-64ea-4198-a437-1fd964f39722",
   "metadata": {},
   "outputs": [],
   "source": [
    "gmx.pdb2gmx(f='reference.pdb',o='reference.gro',p='reference.top',water='tip3p',ff='amber99')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 416,
   "id": "9d4f232c-1b16-489f-b05c-2bf425e0724c",
   "metadata": {},
   "outputs": [],
   "source": [
    "with open('min.mdp','w') as m:\n",
    "    m.write('''\n",
    "integrator  = steep         ; Algorithm (steep = steepest descent minimization)\n",
    "emtol       = 1000.0        ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm\n",
    "emstep      = 0.01          ; Minimization step size\n",
    "nsteps      = 50000         ; Maximum number of (minimization) steps to perform\n",
    "\n",
    "nstxout                 = 1         \n",
    "nstvout                 = 0         \n",
    "nstfout                 = 0         \n",
    "nstlog                  = 5\n",
    "nstxout-compressed      = 1\n",
    "\n",
    "; Parameters describing how to find the neighbors of each atom and how to calculate the interactions\n",
    "nstlist         = 1         ; Frequency to update the neighbor list and long range forces\n",
    "cutoff-scheme   = Verlet    ; Buffered neighbor searching\n",
    "ns_type         = grid      ; Method to determine neighbor list (simple, grid)\n",
    "coulombtype     = Cut-off   ; Treatment of long range electrostatic interactions\n",
    "rcoulomb        = 1.0       ; Short-range electrostatic cut-off\n",
    "rvdw            = 1.0       ; Short-range Van der Waals cut-off\n",
    "pbc             = xyz       ; Periodic Boundary Conditions in all 3 dimensions\n",
    "\n",
    "disre           = Simple\n",
    "define                  = -DPOSRES \n",
    "''')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 417,
   "id": "934e8c42-3a9c-4197-972a-db1a4cfb1b1e",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "pod/asmsa-gmx-13210-5qp5d condition met\n",
      "             :-) GROMACS - gmx grompp, 2023.2-plumed_2.10.0_dev (-:\n",
      "\n",
      "Executable:   /gromacs/AVX2_256_ts/bin/gmx\n",
      "Data prefix:  /gromacs/AVX2_256_ts\n",
      "Working dir:  /mnt/ASMSA\n",
      "Command line:\n",
      "  gmx grompp -f min.mdp -c min.gro -p reference.top -o min.tpr -maxwarn 100000\n",
      "\n",
      "Ignoring obsolete mdp entry 'ns_type'\n",
      "\n",
      "NOTE 1 [file min.mdp]:\n",
      "  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note\n",
      "  that with the Verlet scheme, nstlist has no effect on the accuracy of\n",
      "  your simulation.\n",
      "\n",
      "Generating 1-4 interactions: fudge = 0.5\n",
      "\n",
      "NOTE 2 [file reference.top, line 2668]:\n",
      "  System has non-zero total charge: -1.000000\n",
      "  Total charge should normally be an integer. See\n",
      "  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic\n",
      "  for discussion on how close it should be to an integer.\n",
      "\n",
      "\n",
      "\n",
      "atom name 2 in reference.top and min.gro does not match (H1 - H)\n",
      "\n",
      "atom name 8 in reference.top and min.gro does not match (HB1 - HB3)\n",
      "\n",
      "atom name 30 in reference.top and min.gro does not match (HB1 - HB3)\n",
      "\n",
      "atom name 61 in reference.top and min.gro does not match (HB1 - HB3)\n",
      "\n",
      "atom name 64 in reference.top and min.gro does not match (HG1 - HG3)\n",
      "\n",
      "atom name 78 in reference.top and min.gro does not match (HB1 - HB3)\n",
      "\n",
      "atom name 102 in reference.top and min.gro does not match (HB1 - HB3)\n",
      "\n",
      "atom name 131 in reference.top and min.gro does not match (HB1 - HB3)\n",
      "\n",
      "atom name 141 in reference.top and min.gro does not match (HA1 - HA3)\n",
      "\n",
      "atom name 148 in reference.top and min.gro does not match (HA1 - HA3)\n",
      "\n",
      "atom name 154 in reference.top and min.gro does not match (HD1 - HD3)\n",
      "\n",
      "atom name 157 in reference.top and min.gro does not match (HG1 - HG3)\n",
      "\n",
      "atom name 160 in reference.top and min.gro does not match (HB1 - HB3)\n",
      "\n",
      "atom name 171 in reference.top and min.gro does not match (HB1 - HB3)\n",
      "\n",
      "atom name 182 in reference.top and min.gro does not match (HB1 - HB3)\n",
      "\n",
      "atom name 191 in reference.top and min.gro does not match (HA1 - HA3)\n",
      "\n",
      "atom name 200 in reference.top and min.gro does not match (HB1 - HB3)\n",
      "\n",
      "atom name 203 in reference.top and min.gro does not match (HG1 - HG3)\n",
      "\n",
      "atom name 206 in reference.top and min.gro does not match (HD1 - HD3)\n",
      "\n",
      "atom name 221 in reference.top and min.gro does not match (HD1 - HD3)\n",
      "\n",
      "(more than 20 non-matching atom names)\n",
      "\n",
      "WARNING 1 [file reference.top, line 2668]:\n",
      "  31 non-matching atom names\n",
      "  atom names from reference.top will be used\n",
      "  atom names from min.gro will be ignored\n",
      "\n",
      "\n",
      "Number of degrees of freedom in T-Coupling group rest is 813.00\n",
      "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n",
      "\n",
      "NOTE 3 [file min.mdp]:\n",
      "  You are using a plain Coulomb cut-off, which might produce artifacts.\n",
      "  You might want to consider using PME electrostatics.\n",
      "\n",
      "\n",
      "\n",
      "There were 3 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up min.tpr to ./#min.tpr.57#\n",
      "\n",
      "GROMACS reminds you: \"Give a Man a Fish\" (Arrested Development)\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -1611137289\n",
      "\n",
      "Generated 2145 of the 2145 non-bonded parameter combinations\n",
      "\n",
      "Generated 2145 of the 2145 1-4 parameter combinations\n",
      "\n",
      "Excluding 3 bonded neighbours molecule type 'Protein'\n",
      "\n",
      "atom name 2 in reference.top and min.gro does not match (H1 - H)\n",
      "\n",
      "atom name 8 in reference.top and min.gro does not match (HB1 - HB3)\n",
      "\n",
      "atom name 30 in reference.top and min.gro does not match (HB1 - HB3)\n",
      "\n",
      "atom name 61 in reference.top and min.gro does not match (HB1 - HB3)\n",
      "\n",
      "atom name 64 in reference.top and min.gro does not match (HG1 - HG3)\n",
      "\n",
      "atom name 78 in reference.top and min.gro does not match (HB1 - HB3)\n",
      "\n",
      "atom name 102 in reference.top and min.gro does not match (HB1 - HB3)\n",
      "\n",
      "atom name 131 in reference.top and min.gro does not match (HB1 - HB3)\n",
      "\n",
      "atom name 141 in reference.top and min.gro does not match (HA1 - HA3)\n",
      "\n",
      "atom name 148 in reference.top and min.gro does not match (HA1 - HA3)\n",
      "\n",
      "atom name 154 in reference.top and min.gro does not match (HD1 - HD3)\n",
      "\n",
      "atom name 157 in reference.top and min.gro does not match (HG1 - HG3)\n",
      "\n",
      "atom name 160 in reference.top and min.gro does not match (HB1 - HB3)\n",
      "\n",
      "atom name 171 in reference.top and min.gro does not match (HB1 - HB3)\n",
      "\n",
      "atom name 182 in reference.top and min.gro does not match (HB1 - HB3)\n",
      "\n",
      "atom name 191 in reference.top and min.gro does not match (HA1 - HA3)\n",
      "\n",
      "atom name 200 in reference.top and min.gro does not match (HB1 - HB3)\n",
      "\n",
      "atom name 203 in reference.top and min.gro does not match (HG1 - HG3)\n",
      "\n",
      "atom name 206 in reference.top and min.gro does not match (HD1 - HD3)\n",
      "\n",
      "atom name 221 in reference.top and min.gro does not match (HD1 - HD3)\n",
      "\n",
      "(more than 20 non-matching atom names)\n",
      "Analysing residue names:\n",
      "There are:    20    Protein residues\n",
      "Analysing Protein...\n",
      "\n",
      "This run will generate roughly 252 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "pod/asmsa-gmx-13210-5qp5d condition met\n",
      "             :-) GROMACS - gmx mdrun, 2023.2-plumed_2.10.0_dev (-:\n",
      "\n",
      "Executable:   /gromacs/AVX2_256_ts/bin/gmx\n",
      "Data prefix:  /gromacs/AVX2_256_ts\n",
      "Working dir:  /mnt/ASMSA\n",
      "Command line:\n",
      "  gmx mdrun -deffnm min\n",
      "\n",
      "\n",
      "Back Off! I just backed up min.log to ./#min.log.58#\n",
      "Reading file min.tpr, VERSION 2023.2-plumed_2.10.0_dev (single precision)\n",
      "Using 1 MPI process\n",
      "\n",
      "Non-default thread affinity set, disabling internal thread affinity\n",
      "\n",
      "Using 1 OpenMP thread \n",
      "\n",
      "\n",
      "Back Off! I just backed up min.trr to ./#min.trr.58#\n",
      "\n",
      "Back Off! I just backed up min.edr to ./#min.edr.58#\n",
      "\n",
      "Steepest Descents:\n",
      "   Tolerance (Fmax)   =  1.00000e+03\n",
      "   Number of steps    =        50000\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 102 ms, sys: 147 ms, total: 249 ms\n",
      "Wall time: 9.5 s\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "writing lowest energy coordinates.\n",
      "\n",
      "Back Off! I just backed up min.gro to ./#min.gro.59#\n",
      "\n",
      "Steepest Descents converged to Fmax < 1000 in 4757 steps\n",
      "Potential Energy  =  5.9947646e+03\n",
      "Maximum force     =  9.9673242e+02 on atom 117\n",
      "Norm of force     =  2.4989255e+02\n",
      "\n",
      "GROMACS reminds you: \"I can't relate to you\" (Bad Religion)\n",
      "\n"
     ]
    }
   ],
   "source": [
    "%%time \n",
    "n = 123\n",
    "for n in range(123,124):\n",
    "    with open('posre.itp','w') as p:\n",
    "        p.write('[ dihedral_restraints ]\\n')\n",
    "        for i in range(0,len(ndx)-3):\n",
    "            p.write('  '.join(map(str,ndx[i:i+4])))\n",
    "            p.write(f' 1 {dihs[i,n]} 0 5000\\n')\n",
    "    \n",
    "    gtr = tr3[n]\n",
    "    gtr.save_gro('min.gro')\n",
    "    \n",
    "    gmx.grompp(f='min.mdp',c='min.gro',p='reference.top',o='min.tpr',maxwarn=100000)\n",
    "    \n",
    "    gmx.mdrun(deffnm='min')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "89ca1ea1-0019-4970-a35f-9e5e31d6537e",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 419,
   "id": "44f31e2e-3f39-4fd1-82f6-94b8feaaa6a3",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "0b5cbdf47d1c42ecade286f4fedca93a",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "v=nv.show_file('min.gro')\n",
    "v.add_representation('licorice')\n",
    "v"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "7cae2516-64b5-4114-ad16-90c3a821ddaf",
   "metadata": {},
   "outputs": [],
   "source": [
    "v2=nv.show_mdtraj(tr3[n])\n",
    "v2.add_representation('licorice')\n",
    "v2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "12aaac7e-739c-4f3e-9e3f-03cd6fa01789",
   "metadata": {},
   "outputs": [],
   "source": [
    "gmx.gangle(f='min.gro',n='angle.ndx',g1='dihedral',group1='dihedrals',oall='min.xvg')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e377d2ba-7f8c-4af4-94af-989dfe3d2004",
   "metadata": {},
   "outputs": [],
   "source": [
    "!cat min.xvg"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c449b345-4496-4ca0-b476-321872041f30",
   "metadata": {},
   "outputs": [],
   "source": [
    "dihs[:,n]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "caa9699d-0a9f-4de4-b2d5-5758474dfae9",
   "metadata": {},
   "outputs": [],
   "source": [
    "gmx.energy(f='min.edr',input=['Potential','Dih.-Rest.'],o='emin.xvg')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "847851af-fd83-43bd-8f09-d80f72d07f13",
   "metadata": {},
   "outputs": [],
   "source": [
    "import matplotlib.pyplot as plt\n",
    "energ = np.loadtxt('emin.xvg',comments=['#','@'])\n",
    "plt.plot(energ[:,1],label='Dih.-Rest.')\n",
    "plt.plot(energ[:,2],label='Potential')\n",
    "plt.plot(energ[:,2]-energ[:,1],label='Net')\n",
    "plt.yscale('log')\n",
    "plt.legend()\n",
    "plt.show()\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "64c25b07-d6c2-4ad4-bb80-bd0196bb2965",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 420,
   "id": "8d040efa-bc24-4f63-9e96-bf40ce7f4a5c",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "4ac2bdfd72934f30a1bc51d8b27231b6",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget(max_frame=3762)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "mtr = md.load('min.trr',top=pdb)\n",
    "mtr.xyz = mtr.xyz[-1:0:-1]\n",
    "v = nv.show_mdtraj(mtr)\n",
    "v.add_representation('licorice')\n",
    "v"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 412,
   "id": "9a04a42b-48e6-4bac-8021-bccda8f6202b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(1, 272, 3)"
      ]
     },
     "execution_count": 412,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mtr.xyz.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e699ce32-5912-49af-8df3-fed306b3a29c",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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