rfdiffusion_aa.ipynb

{
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "<a href=\"https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "iJsYHgSER7xN"
      },
      "source": [
        "#**RFdiffusion aa**\n",
        "RFdiffusion aa is a method for structure generation, with or without conditional information (a motif, target etc). It can perform a whole range of protein design challenges as we have outlined in the RFdiffusion [manuscript](https://www.science.org/doi/10.1126/science.adl2528).\n",
        "\n",
        "**<font color=\"red\">NOTE:</font>** This notebook is in development, we are still working on adding all the options from the manuscript above.\n",
        "\n",
        "For **instructions**, see end of Notebook.\n",
        "\n",
        "\n",
        "\n",
        "This is a modified version of Sergey's notebook by Felipe Engelberger, see [original version](https://colab.research.google.com/github/sokrypton/ColabDesign/blob/main/rf/examples/diffusion_ori.ipynb) of this notebook (from 31Mar2023).\n",
        "\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 4,
      "metadata": {
        "cellView": "form",
        "id": "ffOpPfUqHXpb"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "Starting: Installing aria2 for faster downloads\n"
          ]
        },
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "Completed: Installing aria2 for faster downloads\n",
            "Starting: Installing Python dependencies\n",
            "Completed: Installing Python dependencies\n",
            "Starting: Installing DGL\n",
            "Completed: Installing DGL\n",
            "Starting: Installing SE3 Transformer\n",
            "Completed: Installing SE3 Transformer\n",
            "Starting: Downloading and setting up 'ananas'\n",
            "Completed: Downloading and setting up 'ananas'\n",
            "Environment setup complete.\n"
          ]
        }
      ],
      "source": [
        "# @title COLAB ONLY setup **RFdiffusion All Atom** (~5m)\n",
        "#%%time\n",
        "\n",
        "import os\n",
        "import subprocess\n",
        "import time\n",
        "import sys\n",
        "\n",
        "# Function to detect if running on Google Colab\n",
        "def is_colab():\n",
        "    return \"COLAB_GPU\" in os.environ\n",
        "\n",
        "\n",
        "# Base directory setup\n",
        "if is_colab():\n",
        "    BASE_DIR = \"/content\"\n",
        "else:\n",
        "    # For local setup, adjust this path as per your local environment\n",
        "    # By default we will assume you are in the devcontainer path\n",
        "    BASE_DIR = \"/workspaces/all_atom_binder_diffusion\"\n",
        "\n",
        "    # For setups outside the devcontainer, you may need to adjust this path\n",
        "    # BASE_DIR = os.path.expanduser(\"~\")\n",
        "\n",
        "# Adjust paths based on the environment\n",
        "PARAMS_DIR = os.path.join(BASE_DIR, \"params\")\n",
        "RF_DIFFUSION_DIR = os.path.join(BASE_DIR, \"RFdiffusion\")\n",
        "RF_ALL_ATOM_DIR = os.path.join(BASE_DIR, \"rf_diffusion_all_atom\")\n",
        "\n",
        "if 'RFdiffusion' not in sys.path:\n",
        "  os.environ[\"DGLBACKEND\"] = \"pytorch\"\n",
        "  sys.path.append('RFdiffusion')\n",
        "\n",
        "# Ensure the params directory exists\n",
        "os.makedirs(PARAMS_DIR, exist_ok=True)\n",
        "\n",
        "\n",
        "def run_command(command, progress_message, wait=True):\n",
        "    \"\"\"\n",
        "    Run a system command with a progress message.\n",
        "    If wait is False, the command is executed in the background.\n",
        "    \"\"\"\n",
        "    print(f\"Starting: {progress_message}\")\n",
        "    process = subprocess.Popen(\n",
        "        command,\n",
        "        shell=True,\n",
        "        stdout=subprocess.PIPE,\n",
        "        stderr=subprocess.PIPE,\n",
        "        universal_newlines=True,\n",
        "    )\n",
        "    if wait:\n",
        "        stdout, stderr = process.communicate()\n",
        "        # If the return code is an error, print the stderr but do not raise an exception\n",
        "        if process.returncode != 0:\n",
        "            print(f\"Error during {progress_message}: {stderr}\")\n",
        "            raise subprocess.CalledProcessError(process.returncode, command)\n",
        "\n",
        "        print(f\"Completed: {progress_message}\")\n",
        "    return process\n",
        "\n",
        "\n",
        "\n",
        "\n",
        "def setup_environment_colab():\n",
        "    # Install aria2 if not already installed (for faster downloads)\n",
        "    run_command(\"apt-get install -y aria2\", \"Installing aria2 for faster downloads\")\n",
        "\n",
        "    # If parameters are already downloaded, skip the download process\n",
        "    if not os.path.isfile(os.path.join(PARAMS_DIR, \"done.txt\")):\n",
        "        print(\"Downloading parameters and models...\")\n",
        "\n",
        "        # Start downloading parameters and models in the background\n",
        "        download_process = run_command(\n",
        "            f\"cd {PARAMS_DIR} && aria2c -q -x 16 https://files.ipd.uw.edu/krypton/schedules.zip && \\\n",
        "            aria2c -q -x 16 http://files.ipd.uw.edu/pub/RF-All-Atom/weights/RFDiffusionAA_paper_weights.pt && \\\n",
        "            touch done.txt\",\n",
        "            \"Downloading and extracting parameters\", wait=False)\n",
        "#            aria2c -q -x 16 https://storage.googleapis.com/alphafold/alphafold_params_2022-12-06.tar && \\\n",
        "#            tar -xf alphafold_params_2022-12-06.tar && \\\n",
        "\n",
        "\n",
        "    # Install Open Babel if not already installed\n",
        "    if not os.path.isfile(\"/usr/bin/obabel\"):\n",
        "        run_command(\n",
        "            \"apt-get update && apt-get install -y openbabel libopenbabel-dev && ln -s /usr/include/openbabel3 /usr/local/include/openbabel3\",\n",
        "            \"Installing Open Babel and its development files\",\n",
        "        )\n",
        "\n",
        "    # Install SWIG\n",
        "    if not os.path.isfile(\"/usr/bin/swig\"):\n",
        "        run_command(\n",
        "            \"apt-get remove -y swig && apt-get install -y swig3.0 && ln -sf /usr/bin/swig3.0 /usr/bin/swig\",\n",
        "            \"Installing SWIG\",\n",
        "        )\n",
        "\n",
        "    # Install Python dependencies\n",
        "    run_command(\n",
        "        \"pip install jedi omegaconf hydra-core icecream pyrsistent assertpy deepdiff fire git+https://github.com/sokrypton/ColabDesign.git@v1.1.1 py3Dmol openbabel\",\n",
        "        \"Installing Python dependencies\",\n",
        "    )\n",
        "\n",
        "    # Clone RFdiffusion repository\n",
        "    if not os.path.isdir(RF_DIFFUSION_DIR):\n",
        "        run_command(\n",
        "            f\"git clone --branch max https://github.com/engelberger/RFdiffusion.git {RF_DIFFUSION_DIR}\",\n",
        "            \"Cloning RFdiffusion repository\",\n",
        "        )\n",
        "\n",
        "    # Clone RFdiffusion all atom repository\n",
        "    if not os.path.isdir(RF_ALL_ATOM_DIR):\n",
        "        run_command(\n",
        "            f\"git clone --recurse-submodules --branch colab_march_2024 https://github.com/engelberger/rf_diffusion_all_atom.git {RF_ALL_ATOM_DIR}\",\n",
        "            \"Cloning RFdiffusion all atom repository\",\n",
        "        )\n",
        "\n",
        "    # Install DGL\n",
        "    run_command(\n",
        "        \"pip install dgl -f https://data.dgl.ai/wheels/cu121/repo.html\",\n",
        "        \"Installing DGL\",\n",
        "    )\n",
        "\n",
        "\n",
        "\n",
        "    # Install SE3 Transformer\n",
        "    run_command(\n",
        "        f\"cd {os.path.join(RF_DIFFUSION_DIR, 'env/SE3Transformer')} && pip install -q --no-cache-dir -r requirements.txt && pip install -q .\",\n",
        "        \"Installing SE3 Transformer\",\n",
        "    )\n",
        "\n",
        "    # Download and set execute permissions for 'ananas'\n",
        "    run_command(\n",
        "        f\"wget -qnc https://files.ipd.uw.edu/krypton/ananas -P {BASE_DIR} && chmod +x {os.path.join(BASE_DIR, 'ananas')}\",\n",
        "        \"Downloading and setting up 'ananas'\",\n",
        "    )\n",
        "\n",
        "    # If parameters are already downloaded, skip the download process\n",
        "    if not os.path.isfile(os.path.join(PARAMS_DIR, \"done.txt\")):\n",
        "        # Wait for the download process to complete\n",
        "        download_process.communicate()\n",
        "    print(\"Environment setup complete.\")\n",
        "\n",
        "\n",
        "# Call the setup function\n",
        "setup_environment_colab()"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 6,
      "metadata": {
        "cellView": "form",
        "id": "QZM_Q39_zwN1"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "Output base directory: /root/output/ligand_protein_motif\n",
            "Final output path: /root/output/ligand_protein_motif/sample_1\n",
            "Running command: python ./rf_diffusion_all_atom/run_inference.py --config-name=config --config-dir=/root/output/ligand_protein_motif/sample_1 diffuser.T=25\n",
            "/workspaces/all_atom_binder_diffusion/rf_diffusion_all_atom/util.py:216: UserWarning: Using torch.cross without specifying the dim arg is deprecated.\n",
            "Please either pass the dim explicitly or simply use torch.linalg.cross.\n",
            "The default value of dim will change to agree with that of linalg.cross in a future release. (Triggered internally at ../aten/src/ATen/native/Cross.cpp:63.)\n",
            "Z = torch.cross(Xn,Yn)\n",
            "/usr/local/lib/python3.10/dist-packages/hydra/_internal/defaults_list.py:251: UserWarning: In 'config': Defaults list is missing `_self_`. See https://hydra.cc/docs/1.2/upgrades/1.0_to_1.1/default_composition_order for more information\n",
            "warnings.warn(msg, UserWarning)\n",
            "[2024-04-03 21:53:18,260][inference.model_runners][INFO] - Reading checkpoint from ./params/RFDiffusionAA_paper_weights.pt\n",
            "loading ./params/RFDiffusionAA_paper_weights.pt\n",
            "loaded ./params/RFDiffusionAA_paper_weights.pt\n",
            "OVERRIDING: You are changing diffuser.T from the value this model was trained with.\n",
            "[2024-04-03 21:53:20,994][inference.model_runners][INFO] - Loading checkpoint.\n",
            "[2024-04-03 21:53:21,083][diffusion][INFO] - No IGSO3 cache found at /workspaces/all_atom_binder_diffusion/rf_diffusion_all_atom/cached_schedules/T_25_omega_1000_min_sigma_0_02_min_b_1_5_max_b_2_5_schedule_linear.pkl.\n",
            "[2024-04-03 21:53:21,083][diffusion][INFO] - Calculating IGSO3.\n",
            "[2024-04-03 21:54:14,827][__main__][INFO] - Making design /root/output/ligand_protein_motif/sample_1/sample_0\n",
            "[2024-04-03 21:54:14,827][__main__][INFO] - making design 0 of 0:1\n",
            "[2024-04-03 21:54:14,827][inference.model_runners][INFO] - Using contig: ['100-100']\n",
            "With this beta schedule (linear schedule, beta_0 = 0.08, beta_T = 0.56), alpha_bar_T = 3.613896478782408e-05\n",
            "Calculating chi_beta_T dictionary...\n",
            "Done calculating chi_beta_T dictionaries. They are now cached.\n",
            "Done calculating chi_beta_T, chi_alphas_T, and chi_abars_T dictionaries.\n",
            "[2024-04-03 21:54:32,598][inference.model_runners][INFO] - 21:54:32: Timestep 25, current sequence: ????????????????????????????????????????????????????????????????????????????????????????????????????aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa\n",
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            "[2024-04-03 21:54:54,160][inference.model_runners][INFO] - 21:54:54: Timestep 3, current sequence: ??A??AA??A??A??A???A?K????Q??S???AAAAA?SEQ??AA???S???????AA?AA??G?S?AS?AA??QS?AKA?A??A???A??A???S??Kaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa\n",
            "[2024-04-03 21:54:55,139][inference.model_runners][INFO] - 21:54:55: Timestep 2, current sequence: ??E??SA?AA??A???A?LA?K????S??AS??AAAS???KS??SA???A???????A?AAA??K?Q?AS?AK?A?S??KASA??????AA?AA??S??Kaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa\n",
            "[2024-04-03 21:54:56,116][inference.model_runners][INFO] - 21:54:56: Timestep 1, current sequence: ??E??SAAAA?????AAA?A?K?A??A???S??SSAAS??QQ??SA???S??AAA?A?SAS???K?S?SA??KAAQA??KAAAA?AS?SAA??S?????Saaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa\n",
            "[2024-04-03 21:54:56,117][__main__][INFO] - Finished design in 0.69 minutes\n",
            "[2024-04-03 21:54:56,540][__main__][INFO] - design : /root/output/ligand_protein_motif/sample_1/sample_0.pdb\n",
            "[2024-04-03 21:54:56,540][__main__][INFO] - Xt traj: /root/output/ligand_protein_motif/sample_1/traj/sample_0_Xt-1_traj.pdb\n",
            "[2024-04-03 21:54:56,540][__main__][INFO] - X0 traj: /root/output/ligand_protein_motif/sample_1/traj/sample_0_pX0_traj.pdb\n"
          ]
        }
      ],
      "source": [
        "import os\n",
        "import requests\n",
        "import random\n",
        "import string\n",
        "import yaml\n",
        "import subprocess\n",
        "\n",
        "import shutil\n",
        "import glob\n",
        "\n",
        "\n",
        "# Function to detect if running on Google Colab\n",
        "def is_colab():\n",
        "    return \"COLAB_GPU\" in os.environ\n",
        "\n",
        "# Base directory setup\n",
        "BASE_DIR = \"/content\" if is_colab() else os.path.expanduser(\"~\")\n",
        "INPUT_DIR = os.path.join(BASE_DIR, \"input\")\n",
        "OUTPUT_DIR = os.path.join(BASE_DIR, \"output\")\n",
        "\n",
        "# Ensure the input and output directories exist\n",
        "os.makedirs(INPUT_DIR, exist_ok=True)\n",
        "os.makedirs(OUTPUT_DIR, exist_ok=True)\n",
        "\n",
        "def download_pdb(pdb_code, output_dir=INPUT_DIR):\n",
        "    \"\"\"\n",
        "    Download a PDB file given a PDB code.\n",
        "    \"\"\"\n",
        "    url = f\"https://files.rcsb.org/download/{pdb_code}.pdb\"\n",
        "    response = requests.get(url)\n",
        "    if response.status_code == 200:\n",
        "        pdb_path = os.path.join(output_dir, f\"{pdb_code}.pdb\")\n",
        "        with open(pdb_path, 'w') as file:\n",
        "            file.write(response.text)\n",
        "        return pdb_path\n",
        "    else:\n",
        "        raise ValueError(f\"Failed to download PDB file for {pdb_code}\")\n",
        "\n",
        "def handle_pdb_input(pdb_input_type, pdb_code=None, custom_path=None, output_dir=INPUT_DIR):\n",
        "    \"\"\"\n",
        "    Handle PDB input by either uploading a file or downloading it using a PDB code.\n",
        "    \"\"\"\n",
        "    if pdb_input_type == \"upload\":\n",
        "        if is_colab():\n",
        "            from google.colab import files\n",
        "            uploaded = files.upload()\n",
        "            pdb_filename = next(iter(uploaded))\n",
        "            pdb_path = os.path.join(output_dir, pdb_filename)\n",
        "            with open(pdb_path, 'wb') as file:\n",
        "                file.write(uploaded[pdb_filename])\n",
        "            return pdb_path\n",
        "        else:\n",
        "            raise EnvironmentError(\"File upload is only supported on Google Colab.\")\n",
        "    elif pdb_input_type == \"pdb_code\":\n",
        "        return download_pdb(pdb_code, output_dir)\n",
        "    \n",
        "    elif pdb_input_type == \"custom_path\":\n",
        "        if custom_path is not None:\n",
        "          return custom_path\n",
        " \n",
        "    else:\n",
        "        raise ValueError(\"Invalid PDB input type\")\n",
        "\n",
        "def run_rfdiffusion_all_atom(config, output_subfolder=\"ligand_protein_motif\", output_prefix=\"sample\", show_last_n_lines=5, save_stdout=True):\n",
        "    \"\"\"\n",
        "    Wrapper function to run rfdiffusion all atom with specified options, using a YAML configuration file.\n",
        "    The configuration is passed as a dictionary.\n",
        "    \"\"\"\n",
        "    # Generate a base output directory name without duplicating parts of the path\n",
        "    base_output_path = os.path.join(OUTPUT_DIR, output_subfolder)\n",
        "    print(f\"Output base directory: {base_output_path}\")\n",
        "\n",
        "    # Initialize counter to generate a unique output directory\n",
        "    counter = 0\n",
        "    unique_output_path = f\"{base_output_path}/{output_prefix}_{counter}\"\n",
        "    while os.path.exists(unique_output_path):\n",
        "        counter += 1\n",
        "        unique_output_path = f\"{base_output_path}/{output_prefix}_{counter}\"\n",
        "\n",
        "    final_output_path = unique_output_path\n",
        "    print(f\"Final output path: {final_output_path}\")\n",
        "    # Ensure the final output directory exists\n",
        "    os.makedirs(final_output_path, exist_ok=True)\n",
        "\n",
        "    # Update the output_prefix in the config with the actual output path\n",
        "    config[\"inference\"][\"output_prefix\"] = os.path.join(final_output_path, output_prefix)\n",
        "\n",
        "    # Write the configuration to a YAML file inside the correct output directory\n",
        "    config_filename = \"config.yaml\"  # Configuration file name\n",
        "    config_file_path = os.path.join(final_output_path, config_filename)  # Full path to the configuration file\n",
        "    with open(config_file_path, 'w') as file:\n",
        "        yaml.dump(config, file)\n",
        "\n",
        "    # Correct the command to run the inference script with the YAML config file\n",
        "    cmd = [\n",
        "        \"python\", \"./rf_diffusion_all_atom/run_inference.py\",\n",
        "        f\"--config-name={config_filename[:-5]}\",  # Remove the '.yaml' extension\n",
        "        f\"--config-dir={final_output_path}\",\n",
        "        f\"diffuser.T={config['diffuser']['T']}\" # I do not know why this need to be added again if its already in the config.yaml\n",
        "    ]\n",
        "\n",
        "    # Print the command to the console\n",
        "    print(f\"Running command: {' '.join(cmd)}\")\n",
        "\n",
        "    # Initialize a list to keep track of the output lines\n",
        "    output_lines = []\n",
        "\n",
        "    # Use subprocess.Popen to run the command and capture stdout in real-time\n",
        "    process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, universal_newlines=True)\n",
        "\n",
        "    # Correct the path for the log file to ensure it's saved in the final_output_path\n",
        "    if save_stdout:\n",
        "        log_file_path = os.path.join(final_output_path, \"run_inference.log\")  # Corrected path\n",
        "        log_file = open(log_file_path, \"w\")\n",
        "\n",
        "    # Periodically check for new output\n",
        "    while True:\n",
        "        output = process.stdout.readline()\n",
        "        if output == '' and process.poll() is not None:\n",
        "            break\n",
        "        if output:\n",
        "            output_lines.append(output.strip())\n",
        "            # Save to log file if required\n",
        "            if save_stdout:\n",
        "                log_file.write(output)\n",
        "\n",
        "            # Display the last N lines if required\n",
        "            if show_last_n_lines > 0:\n",
        "                display_lines = output_lines[-show_last_n_lines:]\n",
        "                print(\"\\n\".join(display_lines))\n",
        "\n",
        "        # time.sleep(1)  # Adjust the sleep time as needed\n",
        "\n",
        "    # Ensure the process has finished and close the log file if it was opened\n",
        "    process.poll()\n",
        "    if save_stdout:\n",
        "        log_file.close()\n",
        "\n",
        "\n",
        "    return final_output_path\n",
        "\n",
        "\n",
        "\n",
        "#@title ### Small molecule binder design with protein motif\n",
        "\n",
        "# Interface for specifying PDB input\n",
        "pdb_input_type = \"pdb_code\" #@param [\"upload\", \"pdb_code\", \"manual_path\"]\n",
        "pdb_code = \"7v11\" #@param {type:\"string\"}\n",
        "custom_path = \"\" #@param {type:\"string\"}\n",
        "\n",
        "if pdb_input_type == \"pdb_code\":\n",
        "    input_pdb = handle_pdb_input(pdb_input_type, pdb_code)\n",
        "elif pdb_input_type == \"upload\":\n",
        "    print(\"Please upload your PDB file:\")\n",
        "    # Assuming running in Colab\n",
        "    input_pdb = handle_pdb_input(pdb_input_type)\n",
        "elif pdb_input_type == \"custom_path\":\n",
        "    input_pdb = handle_pdb_input(pdb_input_type, pdb_code, custom_path)\n",
        "\n",
        "\n",
        "contigs = \"100-100\" #@param {type:\"string\"}\n",
        "contig_length = \"\" #@param {type:\"string\"}\n",
        "ligand = \"OQO\" #@param {type:\"string\"}\n",
        "num_designs = 1 #@param {type:\"integer\"}\n",
        "design_startnum = 0 #@param {type:\"integer\"}\n",
        "output_prefix = \"sample\" #@param {type:\"string\"}\n",
        "output_subfolder = \"ligand_protein_motif\" #@param {type:\"string\"}\n",
        "\n",
        "deterministic = True #@param {type:\"boolean\"}\n",
        "T = 25 #@param {type:\"integer\"}\n",
        "\n",
        "# Split contigs string into list\n",
        "contigs_list = contigs.split(',')\n",
        "\n",
        "# Convert contigs list to string format for YAML\n",
        "contigs_yaml = [f\"{contig}\" for contig in contigs_list]\n",
        "contig_length = contig_length if contig_length else None\n",
        "\n",
        "# Define the configuration dictionary based on the user inputs\n",
        "config = {\n",
        "    \"inference\": {\n",
        "        \"deterministic\": deterministic,\n",
        "        \"input_pdb\": input_pdb,\n",
        "        \"ligand\": ligand,\n",
        "        \"num_designs\": num_designs,\n",
        "        \"design_startnum\": design_startnum,\n",
        "        \"ckpt_path\": \"./params/RFDiffusionAA_paper_weights.pt\",\n",
        "        \"model_runner\": \"NRBStyleSelfCond\"\n",
        "    },\n",
        "    \"diffuser\": {\n",
        "        \"T\": T\n",
        "    },\n",
        "    \"contigmap\": {\n",
        "        \"contigs\": contigs_yaml,\n",
        "        \"length\": contig_length\n",
        "    },\n",
        "    \"model\": {\"freeze_track_motif\": \"True\"},\n",
        "    \"defaults\": [\"aa\"]\n",
        "}\n",
        "\n",
        "# Specify additional options for the run function\n",
        "show_last_n_lines = 1  # Show only the last 1 lines of stdout to avoid cluttering the notebook, above 1 is not working at the moment\n",
        "save_stdout = True  # Save the stdout as a logfile in the output folder\n",
        "\n",
        "# Call the run_rfdiffusion_all_atom function with the specified configuration and options\n",
        "final_output_path = run_rfdiffusion_all_atom(config, output_subfolder=output_subfolder, output_prefix=output_prefix, show_last_n_lines=show_last_n_lines, save_stdout=save_stdout)\n",
        "\n",
        "#@markdown After running the diffusion function, you can zip the last job's output for download:\n",
        "\n",
        "#@markdown Run the following cell to zip and download the last job's output."
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 7,
      "metadata": {
        "cellView": "form",
        "id": "WcQD7Mk3en3i"
      },
      "outputs": [
        {
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-0.396  1.00  0.00\\nATOM    112  CA  LYS A  22      17.262   9.557  -0.074  1.00  0.00\\nATOM    113  C   LYS A  22      16.186   9.972  -1.069  1.00  0.00\\nATOM    114  O   LYS A  22      15.790  11.143  -1.135  1.00  0.00\\nATOM    115  CB  LYS A  22       0.000   0.000   0.000  1.00  0.00\\nATOM    116  CG  LYS A  22       0.000   0.000   0.000  1.00  0.00\\nATOM    117  CD  LYS A  22       0.000   0.000   0.000  1.00  0.00\\nATOM    118  CE  LYS A  22       0.000   0.000   0.000  1.00  0.00\\nATOM    119  NZ  LYS A  22       0.000   0.000   0.000  1.00  0.00\\nATOM    120  N   ALA A  23      15.727   8.989  -1.836  1.00  0.00\\nATOM    121  CA  ALA A  23      14.687   9.324  -2.801  1.00  0.00\\nATOM    122  C   ALA A  23      13.312   9.342  -2.146  1.00  0.00\\nATOM    123  O   ALA A  23      13.072   8.519  -1.253  1.00  0.00\\nATOM    124  CB  ALA A  23       0.000   0.000   0.000  1.00  0.00\\nATOM    125  N   ALA A  24      12.476  10.152  -2.501  1.00  0.00\\nATOM    126  CA  ALA A  24      11.116  10.172  -1.976  1.00  0.00\\nATOM    127  C   ALA A  24      10.211   9.226  -2.755  1.00  0.00\\nATOM    128  O   ALA A  24      10.501   8.993  -3.936  1.00  0.00\\nATOM    129  CB  ALA A  24       0.000   0.000   0.000  1.00  0.00\\nATOM    130  N   ALA A  25       9.220   8.703  -2.237  1.00  0.00\\nATOM    131  CA  ALA A  25       8.333   7.766  -2.916  1.00  0.00\\nATOM    132  C   ALA A  25       7.762   8.373  -4.191  1.00  0.00\\nATOM    133  O   ALA A  25       7.574   7.655  -5.181  1.00  0.00\\nATOM    134  CB  ALA A  25       0.000   0.000   0.000  1.00  0.00\\nATOM    135  N   ALA A  26       7.488   9.655  -4.188  1.00  0.00\\nATOM    136  CA  ALA A  26       6.917  10.326  -5.349  1.00  0.00\\nATOM    137  C   ALA A  26       7.919  10.393  -6.495  1.00  0.00\\nATOM    138  O   ALA A  26       7.580  10.172  -7.664  1.00  0.00\\nATOM    139  CB  ALA A  26       0.000   0.000   0.000  1.00  0.00\\nATOM    140  N   ALA A  27       9.191  10.714  -6.109  1.00  0.00\\nATOM    141  CA  ALA A  27      10.256  10.724  -7.104  1.00  0.00\\nATOM    142  C   ALA A  27      10.514   9.325  -7.649  1.00  0.00\\nATOM    143  O   ALA A  27      10.777   9.152  -8.846  1.00  0.00\\nATOM    144  CB  ALA A  27       0.000   0.000   0.000  1.00  0.00\\nATOM    145  N   ALA A  28      10.437   8.337  -6.765  1.00  0.00\\nATOM    146  CA  ALA A  28      10.623   6.956  -7.193  1.00  0.00\\nATOM    147  C   ALA A  28       9.574   6.552  -8.221  1.00  0.00\\nATOM    148  O   ALA A  28       9.910   5.972  -9.261  1.00  0.00\\nATOM    149  CB  ALA A  28       0.000   0.000   0.000  1.00  0.00\\nATOM    150  N   ALA A  29       8.312   6.855  -7.935  1.00  0.00\\nATOM    151  CA  ALA A  29       7.205   6.463  -8.799  1.00  0.00\\nATOM    152  C   ALA A  29       7.286   7.162 -10.150  1.00  0.00\\nATOM    153  O   ALA A  29       7.039   6.556 -11.200  1.00  0.00\\nATOM    154  CB  ALA A  29       0.000   0.000   0.000  1.00  0.00\\nATOM    155  N   ALA A  30       7.648   8.488 -10.096  1.00  0.00\\nATOM    156  CA  ALA A  30       7.804   9.252 -11.328  1.00  0.00\\nATOM    157  C   ALA A  30       8.917   8.678 -12.195  1.00  0.00\\nATOM    158  O   ALA A  30       8.751   8.559 -13.416  1.00  0.00\\nATOM    159  CB  ALA A  30       0.000   0.000   0.000  1.00  0.00\\nATOM    160  N   SER A  31      10.013   8.333 -11.602  1.00  0.00\\nATOM    161  CA  SER A  31      11.146   7.829 -12.369  1.00  0.00\\nATOM    162  C   SER A  31      10.871   6.429 -12.902  1.00  0.00\\nATOM    163  O   SER A  31      11.287   6.073 -14.011  1.00  0.00\\nATOM    164  CB  SER A  31       0.000   0.000   0.000  1.00  0.00\\nATOM    165  OG  SER A  31       0.000   0.000   0.000  1.00  0.00\\nATOM    166  N   ALA A  32      10.149   5.630 -12.072  1.00  0.00\\nATOM    167  CA  ALA A  32       9.783   4.283 -12.493  1.00  0.00\\nATOM    168  C   ALA A  32       8.824   4.317 -13.676  1.00  0.00\\nATOM    169  O   ALA A  32       8.935   3.516 -14.613  1.00  0.00\\nATOM    170  CB  ALA A  32       0.000   0.000   0.000  1.00  0.00\\nATOM    171  N   ALA A  33       7.858   5.285 -13.609  1.00  0.00\\nATOM    172  CA  ALA A  33       6.892   5.443 -14.690  1.00  0.00\\nATOM    173  C   ALA A  33       7.582   5.822 -15.994  1.00  0.00\\nATOM    174  O   ALA A  33       7.255   5.291 -17.063  1.00  0.00\\nATOM    175  CB  ALA A  33       0.000   0.000   0.000  1.00  0.00\\nATOM    176  N   SER A  34       8.548   6.755 -15.889  1.00  0.00\\nATOM    177  CA  SER A  34       9.239   7.212 -17.089  1.00  0.00\\nATOM    178  C   SER A  34      10.080   6.098 -17.698  1.00  0.00\\nATOM    179  O   SER A  34      10.188   5.995 -18.927  1.00  0.00\\nATOM    180  CB  SER A  34       0.000   0.000   0.000  1.00  0.00\\nATOM    181  OG  SER A  34       0.000   0.000   0.000  1.00  0.00\\nATOM    182  N   SER A  35      10.683   5.255 -16.831  1.00  0.00\\nATOM    183  CA  SER A  35      11.503   4.152 -17.318  1.00  0.00\\nATOM    184  C   SER A  35      10.643   3.061 -17.943  1.00  0.00\\nATOM    185  O   SER A  35      11.025   2.449 -18.949  1.00  0.00\\nATOM    186  CB  SER A  35       0.000   0.000   0.000  1.00  0.00\\nATOM    187  OG  SER A  35       0.000   0.000   0.000  1.00  0.00\\nATOM    188  N   ALA A  36       9.486   2.828 -17.336  1.00  0.00\\nATOM    189  CA  ALA A  36       8.533   1.860 -17.865  1.00  0.00\\nATOM    190  C   ALA A  36       7.954   2.327 -19.195  1.00  0.00\\nATOM    191  O   ALA A  36       7.715   1.521 -20.103  1.00  0.00\\nATOM    192  CB  ALA A  36       0.000   0.000   0.000  1.00  0.00\\nATOM    193  N   ALA A  37       7.727   3.689 -19.294  1.00  0.00\\nATOM    194  CA  ALA A  37       7.200   4.262 -20.527  1.00  0.00\\nATOM    195  C   ALA A  37       8.176   4.077 -21.682  1.00  0.00\\nATOM    196  O   ALA A  37       7.776   3.954 -22.846  1.00  0.00\\nATOM    197  CB  ALA A  37       0.000   0.000   0.000  1.00  0.00\\nATOM    198  N   SER A  38       9.495   4.060 -21.322  1.00  0.00\\nATOM    199  CA  SER A  38      10.520   3.837 -22.335  1.00  0.00\\nATOM    200  C   SER A  38      10.499   2.397 -22.832  1.00  0.00\\nATOM    201  O   SER A  38      10.849   2.117 -23.986  1.00  0.00\\nATOM    202  CB  SER A  38       0.000   0.000   0.000  1.00  0.00\\nATOM    203  OG  SER A  38       0.000   0.000   0.000  1.00  0.00\\nATOM    204  N   ALA A  39      10.074   1.474 -21.927  1.00  0.00\\nATOM    205  CA  ALA A  39       9.960   0.069 -22.299  1.00  0.00\\nATOM    206  C   ALA A  39       8.594  -0.233 -22.901  1.00  0.00\\nATOM    207  O   ALA A  39       8.526  -1.027 -23.848  1.00  0.00\\nATOM    208  CB  ALA A  39       0.000   0.000   0.000  1.00  0.00\\nATOM    209  N   ALA A  40       7.469   0.373 -22.393  1.00  0.00\\nATOM    210  CA  ALA A  40       6.105   0.225 -22.885  1.00  0.00\\nATOM    211  C   ALA A  40       5.400   1.573 -22.967  1.00  0.00\\nATOM    212  O   ALA A  40       4.981   2.067 -21.912  1.00  0.00\\nATOM    213  CB  ALA A  40       0.000   0.000   0.000  1.00  0.00\\nATOM    214  N   GLN A  41       5.246   2.155 -24.028  1.00  0.00\\nATOM    215  CA  GLN A  41       4.757   3.512 -24.243  1.00  0.00\\nATOM    216  C   GLN A  41       3.398   3.719 -23.586  1.00  0.00\\nATOM    217  O   GLN A  41       3.171   4.931 -23.484  1.00  0.00\\nATOM    218  CB  GLN A  41       0.000   0.000   0.000  1.00  0.00\\nATOM    219  CG  GLN A  41       0.000   0.000   0.000  1.00  0.00\\nATOM    220  CD  GLN A  41       0.000   0.000   0.000  1.00  0.00\\nATOM    221  OE1 GLN A  41       0.000   0.000   0.000  1.00  0.00\\nATOM    222  NE2 GLN A  41       0.000   0.000   0.000  1.00  0.00\\nATOM    223  N   GLN A  42       2.654   3.162 -23.222  1.00  0.00\\nATOM    224  CA  GLN A  42       1.297   3.321 -22.712  1.00  0.00\\nATOM    225  C   GLN A  42       1.271   3.269 -21.190  1.00  0.00\\nATOM    226  O   GLN A  42       0.173   3.347 -20.624  1.00  0.00\\nATOM    227  CB  GLN A  42       0.000   0.000   0.000  1.00  0.00\\nATOM    228  CG  GLN A  42       0.000   0.000   0.000  1.00  0.00\\nATOM    229  CD  GLN A  42       0.000   0.000   0.000  1.00  0.00\\nATOM    230  OE1 GLN A  42       0.000   0.000   0.000  1.00  0.00\\nATOM    231  NE2 GLN A  42       0.000   0.000   0.000  1.00  0.00\\nATOM    232  N   ALA A  43       2.377   3.145 -20.497  1.00  0.00\\nATOM    233  CA  ALA A  43       2.437   3.045 -19.044  1.00  0.00\\nATOM    234  C   ALA A  43       2.344   4.419 -18.393  1.00  0.00\\nATOM    235  O   ALA A  43       3.021   5.351 -18.844  1.00  0.00\\nATOM    236  CB  ALA A  43       0.000   0.000   0.000  1.00  0.00\\nATOM    237  N   ALA A  44       1.598   4.561 -17.437  1.00  0.00\\nATOM    238  CA  ALA A  44       1.430   5.818 -16.718  1.00  0.00\\nATOM    239  C   ALA A  44       1.658   5.632 -15.223  1.00  0.00\\nATOM    240  O   ALA A  44       1.819   4.489 -14.779  1.00  0.00\\nATOM    241  CB  ALA A  44       0.000   0.000   0.000  1.00  0.00\\nATOM    242  N   SER A  45       1.678   6.687 -14.444  1.00  0.00\\nATOM    243  CA  SER A  45       1.838   6.643 -12.995  1.00  0.00\\nATOM    244  C   SER A  45       0.729   5.828 -12.343  1.00  0.00\\nATOM    245  O   SER A  45       0.991   5.098 -11.378  1.00  0.00\\nATOM    246  CB  SER A  45       0.000   0.000   0.000  1.00  0.00\\nATOM    247  OG  SER A  45       0.000   0.000   0.000  1.00  0.00\\nATOM    248  N   ALA A  46      -0.515   5.937 -12.850  1.00  0.00\\nATOM    249  CA  ALA A  46      -1.649   5.185 -12.325  1.00  0.00\\nATOM    250  C   ALA A  46      -1.395   3.685 -12.395  1.00  0.00\\nATOM    251  O   ALA A  46      -1.635   2.939 -11.436  1.00  0.00\\nATOM    252  CB  ALA A  46       0.000   0.000   0.000  1.00  0.00\\nATOM    253  N   ALA A  47      -0.894   3.265 -13.586  1.00  0.00\\nATOM    254  CA  ALA A  47      -0.618   1.843 -13.749  1.00  0.00\\nATOM    255  C   ALA A  47       0.448   1.373 -12.768  1.00  0.00\\nATOM    256  O   ALA A  47       0.349   0.274 -12.208  1.00  0.00\\nATOM    257  CB  ALA A  47       0.000   0.000   0.000  1.00  0.00\\nATOM    258  N   ALA A  48       1.466   2.211 -12.566  1.00  0.00\\nATOM    259  CA  ALA A  48       2.554   1.854 -11.663  1.00  0.00\\nATOM    260  C   ALA A  48       2.073   1.790 -10.219  1.00  0.00\\nATOM    261  O   ALA A  48       2.473   0.867  -9.498  1.00  0.00\\nATOM    262  CB  ALA A  48       0.000   0.000   0.000  1.00  0.00\\nATOM    263  N   ALA A  49       1.298   2.652  -9.797  1.00  0.00\\nATOM    264  CA  ALA A  49       0.764   2.669  -8.440  1.00  0.00\\nATOM    265  C   ALA A  49      -0.063   1.421  -8.158  1.00  0.00\\nATOM    266  O   ALA A  49       0.063   0.793  -7.099  1.00  0.00\\nATOM    267  CB  ALA A  49       0.000   0.000   0.000  1.00  0.00\\nATOM    268  N   SER A  50      -0.927   1.074  -9.152  1.00  0.00\\nATOM    269  CA  SER A  50      -1.738  -0.129  -9.006  1.00  0.00\\nATOM    270  C   SER A  50      -0.867  -1.377  -8.950  1.00  0.00\\nATOM    271  O   SER A  50      -1.131  -2.299  -8.168  1.00  0.00\\nATOM    272  CB  SER A  50       0.000   0.000   0.000  1.00  0.00\\nATOM    273  OG  SER A  50       0.000   0.000   0.000  1.00  0.00\\nATOM    274  N   ALA A  51       0.133  -1.395  -9.756  1.00  0.00\\nATOM    275  CA  ALA A  51       1.016  -2.555  -9.800  1.00  0.00\\nATOM    276  C   ALA A  51       1.736  -2.750  -8.472  1.00  0.00\\nATOM    277  O   ALA A  51       1.887  -3.879  -7.988  1.00  0.00\\nATOM    278  CB  ALA A  51       0.000   0.000   0.000  1.00  0.00\\nATOM    279  N   ALA A  52       2.172  -1.641  -7.901  1.00  0.00\\nATOM    280  CA  ALA A  52       2.899  -1.694  -6.638  1.00  0.00\\nATOM    281  C   ALA A  52       1.992  -2.140  -5.498  1.00  0.00\\nATOM    282  O   ALA A  52       2.410  -2.929  -4.642  1.00  0.00\\nATOM    283  CB  ALA A  52       0.000   0.000   0.000  1.00  0.00\\nATOM    284  N   ALA A  53       0.788  -1.654  -5.484  1.00  0.00\\nATOM    285  CA  ALA A  53      -0.163  -2.012  -4.438  1.00  0.00\\nATOM    286  C   ALA A  53      -0.545  -3.484  -4.522  1.00  0.00\\nATOM    287  O   ALA A  53      -0.626  -4.184  -3.504  1.00  0.00\\nATOM    288  CB  ALA A  53       0.000   0.000   0.000  1.00  0.00\\nATOM    289  N   ALA A  54      -0.779  -3.939  -5.765  1.00  0.00\\nATOM    290  CA  ALA A  54      -1.161  -5.334  -5.950  1.00  0.00\\nATOM    291  C   ALA A  54      -0.010  -6.271  -5.607  1.00  0.00\\nATOM    292  O   ALA A  54      -0.211  -7.328  -4.996  1.00  0.00\\nATOM    293  CB  ALA A  54       0.000   0.000   0.000  1.00  0.00\\nATOM    294  N   ALA A  55       1.202  -5.866  -6.011  1.00  0.00\\nATOM    295  CA  ALA A  55       2.379  -6.687  -5.752  1.00  0.00\\nATOM    296  C   ALA A  55       2.667  -6.782  -4.259  1.00  0.00\\nATOM    297  O   ALA A  55       3.067  -7.839  -3.755  1.00  0.00\\nATOM    298  CB  ALA A  55       0.000   0.000   0.000  1.00  0.00\\nATOM    299  N   ALA A  56       2.455  -5.648  -3.555  1.00  0.00\\nATOM    300  CA  ALA A  56       2.642  -5.611  -2.110  1.00  0.00\\nATOM    301  C   ALA A  56       1.676  -6.555  -1.405  1.00  0.00\\nATOM    302  O   ALA A  56       2.034  -7.258  -0.451  1.00  0.00\\nATOM    303  CB  ALA A  56       0.000   0.000   0.000  1.00  0.00\\nATOM    304  N   ALA A  57       0.418  -6.540  -1.920  1.00  0.00\\nATOM    305  CA  ALA A  57      -0.594  -7.425  -1.356  1.00  0.00\\nATOM    306  C   ALA A  57      -0.269  -8.886  -1.641  1.00  0.00\\nATOM    307  O   ALA A  57      -0.441  -9.749  -0.771  1.00  0.00\\nATOM    308  CB  ALA A  57       0.000   0.000   0.000  1.00  0.00\\nATOM    309  N   ALA A  58       0.214  -9.165  -2.898  1.00  0.00\\nATOM    310  CA  ALA A  58       0.567 -10.532  -3.261  1.00  0.00\\nATOM    311  C   ALA A  58       1.700 -11.059  -2.389  1.00  0.00\\nATOM    312  O   ALA A  58       1.666 -12.219  -1.961  1.00  0.00\\nATOM    313  CB  ALA A  58       0.000   0.000   0.000  1.00  0.00\\nATOM    314  N   SER A  59       2.705 -10.213  -2.124  1.00  0.00\\nATOM    315  CA  SER A  59       3.822 -10.611  -1.276  1.00  0.00\\nATOM    316  C   SER A  59       3.361 -10.889   0.149  1.00  0.00\\nATOM    317  O   SER A  59       3.839 -11.829   0.796  1.00  0.00\\nATOM    318  CB  SER A  59       0.000   0.000   0.000  1.00  0.00\\nATOM    319  OG  SER A  59       0.000   0.000   0.000  1.00  0.00\\nATOM    320  N   ALA A  60       2.409 -10.045   0.641  1.00  0.00\\nATOM    321  CA  ALA A  60       1.841 -10.253   1.968  1.00  0.00\\nATOM    322  C   ALA A  60       1.130 -11.597   2.058  1.00  0.00\\nATOM    323  O   ALA A  60       1.230 -12.288   3.080  1.00  0.00\\nATOM    324  CB  ALA A  60       0.000   0.000   0.000  1.00  0.00\\nATOM    325  N   SER A  61       0.402 -11.974   0.981  1.00  0.00\\nATOM    326  CA  SER A  61      -0.301 -13.251   0.959  1.00  0.00\\nATOM    327  C   SER A  61       0.677 -14.419   0.954  1.00  0.00\\nATOM    328  O   SER A  61       0.435 -15.444   1.604  1.00  0.00\\nATOM    329  CB  SER A  61       0.000   0.000   0.000  1.00  0.00\\nATOM    330  OG  SER A  61       0.000   0.000   0.000  1.00  0.00\\nATOM    331  N   ALA A  62       1.771 -14.260   0.226  1.00  0.00\\nATOM    332  CA  ALA A  62       2.791 -15.300   0.162  1.00  0.00\\nATOM    333  C   ALA A  62       3.410 -15.550   1.531  1.00  0.00\\nATOM    334  O   ALA A  62       3.666 -16.695   1.925  1.00  0.00\\nATOM    335  CB  ALA A  62       0.000   0.000   0.000  1.00  0.00\\nATOM    336  N   ALA A  63       3.648 -14.409   2.263  1.00  0.00\\nATOM    337  CA  ALA A  63       4.248 -14.473   3.590  1.00  0.00\\nATOM    338  C   ALA A  63       3.319 -15.162   4.581  1.00  0.00\\nATOM    339  O   ALA A  63       3.763 -15.854   5.506  1.00  0.00\\nATOM    340  CB  ALA A  63       0.000   0.000   0.000  1.00  0.00\\nATOM    341  N   ALA A  64       1.983 -14.947   4.354  1.00  0.00\\nATOM    342  CA  ALA A  64       0.995 -15.590   5.212  1.00  0.00\\nATOM    343  C   ALA A  64       0.839 -17.065   4.863  1.00  0.00\\nATOM    344  O   ALA A  64       0.005 -17.733   5.486  1.00  0.00\\nATOM    345  CB  ALA A  64       0.000   0.000   0.000  1.00  0.00\\nATOM    346  N   LYS A  65       1.522 -17.561   3.994  1.00  0.00\\nATOM    347  CA  LYS A  65       1.524 -19.005   3.794  1.00  0.00\\nATOM    348  C   LYS A  65       0.648 -19.399   2.611  1.00  0.00\\nATOM    349  O   LYS A  65       0.324 -20.583   2.459  1.00  0.00\\nATOM    350  CB  LYS A  65       0.000   0.000   0.000  1.00  0.00\\nATOM    351  CG  LYS A  65       0.000   0.000   0.000  1.00  0.00\\nATOM    352  CD  LYS A  65       0.000   0.000   0.000  1.00  0.00\\nATOM    353  CE  LYS A  65       0.000   0.000   0.000  1.00  0.00\\nATOM    354  NZ  LYS A  65       0.000   0.000   0.000  1.00  0.00\\nATOM    355  N   ALA A  66       0.281 -18.495   1.822  1.00  0.00\\nATOM    356  CA  ALA A  66      -0.598 -18.850   0.714  1.00  0.00\\nATOM    357  C   ALA A  66       0.187 -19.466  -0.437  1.00  0.00\\nATOM    358  O   ALA A  66       1.317 -19.037  -0.706  1.00  0.00\\nATOM    359  CB  ALA A  66       0.000   0.000   0.000  1.00  0.00\\nATOM    360  N   SER A  67      -0.365 -20.430  -1.101  1.00  0.00\\nATOM    361  CA  SER A  67       0.323 -20.968  -2.268  1.00  0.00\\nATOM    362  C   SER A  67       0.422 -19.929  -3.377  1.00  0.00\\nATOM    363  O   SER A  67      -0.538 -19.164  -3.534  1.00  0.00\\nATOM    364  CB  SER A  67       0.000   0.000   0.000  1.00  0.00\\nATOM    365  OG  SER A  67       0.000   0.000   0.000  1.00  0.00\\nATOM    366  N   ALA A  68       1.439 -19.838  -4.118  1.00  0.00\\nATOM    367  CA  ALA A  68       1.627 -18.871  -5.193  1.00  0.00\\nATOM    368  C   ALA A  68       0.548 -19.015  -6.259  1.00  0.00\\nATOM    369  O   ALA A  68       0.095 -18.032  -6.859  1.00  0.00\\nATOM    370  CB  ALA A  68       0.000   0.000   0.000  1.00  0.00\\nATOM    371  N   SER A  69       0.146 -20.304  -6.477  1.00  0.00\\nATOM    372  CA  SER A  69      -0.918 -20.531  -7.447  1.00  0.00\\nATOM    373  C   SER A  69      -2.234 -19.928  -6.972  1.00  0.00\\nATOM    374  O   SER A  69      -2.983 -19.383  -7.793  1.00  0.00\\nATOM    375  CB  SER A  69       0.000   0.000   0.000  1.00  0.00\\nATOM    376  OG  SER A  69       0.000   0.000   0.000  1.00  0.00\\nATOM    377  N   ALA A  70      -2.531 -20.007  -5.709  1.00  0.00\\nATOM    378  CA  ALA A  70      -3.734 -19.412  -5.140  1.00  0.00\\nATOM    379  C   ALA A  70      -3.695 -17.892  -5.235  1.00  0.00\\nATOM    380  O   ALA A  70      -4.706 -17.231  -5.502  1.00  0.00\\nATOM    381  CB  ALA A  70       0.000   0.000   0.000  1.00  0.00\\nATOM    382  N   ALA A  71      -2.417 -17.335  -4.993  1.00  0.00\\nATOM    383  CA  ALA A  71      -2.210 -15.895  -5.094  1.00  0.00\\nATOM    384  C   ALA A  71      -2.460 -15.401  -6.513  1.00  0.00\\nATOM    385  O   ALA A  71      -3.092 -14.356  -6.712  1.00  0.00\\nATOM    386  CB  ALA A  71       0.000   0.000   0.000  1.00  0.00\\nATOM    387  N   ALA A  72      -1.952 -16.168  -7.516  1.00  0.00\\nATOM    388  CA  ALA A  72      -2.109 -15.791  -8.916  1.00  0.00\\nATOM    389  C   ALA A  72      -3.567 -15.879  -9.350  1.00  0.00\\nATOM    390  O   ALA A  72      -4.057 -15.053 -10.130  1.00  0.00\\nATOM    391  CB  ALA A  72       0.000   0.000   0.000  1.00  0.00\\nATOM    392  N   LYS A  73      -4.244 -16.907  -8.823  1.00  0.00\\nATOM    393  CA  LYS A  73      -5.656 -17.062  -9.152  1.00  0.00\\nATOM    394  C   LYS A  73      -6.493 -15.953  -8.528  1.00  0.00\\nATOM    395  O   LYS A  73      -7.479 -15.513  -9.132  1.00  0.00\\nATOM    396  CB  LYS A  73       0.000   0.000   0.000  1.00  0.00\\nATOM    397  CG  LYS A  73       0.000   0.000   0.000  1.00  0.00\\nATOM    398  CD  LYS A  73       0.000   0.000   0.000  1.00  0.00\\nATOM    399  CE  LYS A  73       0.000   0.000   0.000  1.00  0.00\\nATOM    400  NZ  LYS A  73       0.000   0.000   0.000  1.00  0.00\\nATOM    401  N   ALA A  74      -6.118 -15.493  -7.332  1.00  0.00\\nATOM    402  CA  ALA A  74      -6.868 -14.436  -6.664  1.00  0.00\\nATOM    403  C   ALA A  74      -6.591 -13.079  -7.298  1.00  0.00\\nATOM    404  O   ALA A  74      -7.447 -12.186  -7.279  1.00  0.00\\nATOM    405  CB  ALA A  74       0.000   0.000   0.000  1.00  0.00\\nATOM    406  N   ALA A  75      -5.347 -12.929  -7.877  1.00  0.00\\nATOM    407  CA  ALA A  75      -5.006 -11.661  -8.510  1.00  0.00\\nATOM    408  C   ALA A  75      -4.968 -11.795 -10.027  1.00  0.00\\nATOM    409  O   ALA A  75      -3.952 -11.465 -10.651  1.00  0.00\\nATOM    410  CB  ALA A  75       0.000   0.000   0.000  1.00  0.00\\nATOM    411  N   GLN A  76      -6.034 -12.264 -10.612  1.00  0.00\\nATOM    412  CA  GLN A  76      -6.165 -12.674 -12.005  1.00  0.00\\nATOM    413  C   GLN A  76      -5.661 -11.589 -12.948  1.00  0.00\\nATOM    414  O   GLN A  76      -4.893 -11.919 -13.860  1.00  0.00\\nATOM    415  CB  GLN A  76       0.000   0.000   0.000  1.00  0.00\\nATOM    416  CG  GLN A  76       0.000   0.000   0.000  1.00  0.00\\nATOM    417  CD  GLN A  76       0.000   0.000   0.000  1.00  0.00\\nATOM    418  OE1 GLN A  76       0.000   0.000   0.000  1.00  0.00\\nATOM    419  NE2 GLN A  76       0.000   0.000   0.000  1.00  0.00\\nATOM    420  N   ALA A  77      -6.028 -10.357 -12.799  1.00  0.00\\nATOM    421  CA  ALA A  77      -5.621  -9.295 -13.712  1.00  0.00\\nATOM    422  C   ALA A  77      -4.112  -9.091 -13.681  1.00  0.00\\nATOM    423  O   ALA A  77      -3.452  -8.816 -14.692  1.00  0.00\\nATOM    424  CB  ALA A  77       0.000   0.000   0.000  1.00  0.00\\nATOM    425  N   ALA A  78      -3.583  -9.252 -12.386  1.00  0.00\\nATOM    426  CA  ALA A  78      -2.146  -9.065 -12.223  1.00  0.00\\nATOM    427  C   ALA A  78      -1.365 -10.190 -12.891  1.00  0.00\\nATOM    428  O   ALA A  78      -0.274 -10.010 -13.448  1.00  0.00\\nATOM    429  CB  ALA A  78       0.000   0.000   0.000  1.00  0.00\\nATOM    430  N   ALA A  79      -2.033 -11.426 -12.791  1.00  0.00\\nATOM    431  CA  ALA A  79      -1.377 -12.610 -13.332  1.00  0.00\\nATOM    432  C   ALA A  79      -1.391 -12.599 -14.855  1.00  0.00\\nATOM    433  O   ALA A  79      -0.501 -13.205 -15.466  1.00  0.00\\nATOM    434  CB  ALA A  79       0.000   0.000   0.000  1.00  0.00\\nATOM    435  N   LYS A  80      -2.310 -11.973 -15.464  1.00  0.00\\nATOM    436  CA  LYS A  80      -2.421 -11.900 -16.916  1.00  0.00\\nATOM    437  C   LYS A  80      -1.389 -10.943 -17.500  1.00  0.00\\nATOM    438  O   LYS A  80      -0.977 -11.055 -18.661  1.00  0.00\\nATOM    439  CB  LYS A  80       0.000   0.000   0.000  1.00  0.00\\nATOM    440  CG  LYS A  80       0.000   0.000   0.000  1.00  0.00\\nATOM    441  CD  LYS A  80       0.000   0.000   0.000  1.00  0.00\\nATOM    442  CE  LYS A  80       0.000   0.000   0.000  1.00  0.00\\nATOM    443  NZ  LYS A  80       0.000   0.000   0.000  1.00  0.00\\nATOM    444  N   ALA A  81      -0.962  -9.922 -16.573  1.00  0.00\\nATOM    445  CA  ALA A  81      -0.047  -8.891 -17.048  1.00  0.00\\nATOM    446  C   ALA A  81       1.318  -9.018 -16.385  1.00  0.00\\nATOM    447  O   ALA A  81       1.992  -7.999 -16.188  1.00  0.00\\nATOM    448  CB  ALA A  81       0.000   0.000   0.000  1.00  0.00\\nATOM    449  N   ALA A  82       1.737 -10.195 -16.044  1.00  0.00\\nATOM    450  CA  ALA A  82       2.977 -10.476 -15.330  1.00  0.00\\nATOM    451  C   ALA A  82       4.177  -9.881 -16.055  1.00  0.00\\nATOM    452  O   ALA A  82       5.219  -9.681 -15.418  1.00  0.00\\nATOM    453  CB  ALA A  82       0.000   0.000   0.000  1.00  0.00\\nATOM    454  N   ALA A  83       4.084  -9.588 -17.350  1.00  0.00\\nATOM    455  CA  ALA A  83       5.130  -8.945 -18.136  1.00  0.00\\nATOM    456  C   ALA A  83       5.384  -7.522 -17.655  1.00  0.00\\nATOM    457  O   ALA A  83       6.488  -6.975 -17.778  1.00  0.00\\nATOM    458  CB  ALA A  83       0.000   0.000   0.000  1.00  0.00\\nATOM    459  N   ALA A  84       4.283  -6.937 -17.091  1.00  0.00\\nATOM    460  CA  ALA A  84       4.442  -5.589 -16.558  1.00  0.00\\nATOM    461  C   ALA A  84       5.333  -5.586 -15.323  1.00  0.00\\nATOM    462  O   ALA A  84       6.089  -4.645 -15.050  1.00  0.00\\nATOM    463  CB  ALA A  84       0.000   0.000   0.000  1.00  0.00\\nATOM    464  N   ALA A  85       5.193  -6.730 -14.571  1.00  0.00\\nATOM    465  CA  ALA A  85       6.009  -6.876 -13.372  1.00  0.00\\nATOM    466  C   ALA A  85       7.485  -7.010 -13.723  1.00  0.00\\nATOM    467  O   ALA A  85       8.351  -6.494 -13.005  1.00  0.00\\nATOM    468  CB  ALA A  85       0.000   0.000   0.000  1.00  0.00\\nATOM    469  N   ALA A  86       7.766  -7.702 -14.824  1.00  0.00\\nATOM    470  CA  ALA A  86       9.128  -7.901 -15.304  1.00  0.00\\nATOM    471  C   ALA A  86       9.762  -6.582 -15.727  1.00  0.00\\nATOM    472  O   ALA A  86      10.937  -6.309 -15.451  1.00  0.00\\nATOM    473  CB  ALA A  86       0.000   0.000   0.000  1.00  0.00\\nATOM    474  N   SER A  87       8.933  -5.767 -16.412  1.00  0.00\\nATOM    475  CA  SER A  87       9.417  -4.478 -16.892  1.00  0.00\\nATOM    476  C   SER A  87       9.705  -3.532 -15.733  1.00  0.00\\nATOM    477  O   SER A  87      10.679  -2.768 -15.735  1.00  0.00\\nATOM    478  CB  SER A  87       0.000   0.000   0.000  1.00  0.00\\nATOM    479  OG  SER A  87       0.000   0.000   0.000  1.00  0.00\\nATOM    480  N   ALA A  88       8.792  -3.623 -14.727  1.00  0.00\\nATOM    481  CA  ALA A  88       8.950  -2.776 -13.551  1.00  0.00\\nATOM    482  C   ALA A  88      10.245  -3.092 -12.814  1.00  0.00\\nATOM    483  O   ALA A  88      10.957  -2.192 -12.350  1.00  0.00\\nATOM    484  CB  ALA A  88       0.000   0.000   0.000  1.00  0.00\\nATOM    485  N   SER A  89      10.531  -4.406 -12.717  1.00  0.00\\nATOM    486  CA  SER A  89      11.750  -4.813 -12.029  1.00  0.00\\nATOM    487  C   SER A  89      12.990  -4.376 -12.799  1.00  0.00\\nATOM    488  O   SER A  89      14.012  -4.016 -12.201  1.00  0.00\\nATOM    489  CB  SER A  89       0.000   0.000   0.000  1.00  0.00\\nATOM    490  OG  SER A  89       0.000   0.000   0.000  1.00  0.00\\nATOM    491  N   ALA A  90      12.884  -4.414 -14.179  1.00  0.00\\nATOM    492  CA  ALA A  90      13.996  -4.005 -15.029  1.00  0.00\\nATOM    493  C   ALA A  90      14.226  -2.501 -14.950  1.00  0.00\\nATOM    494  O   ALA A  90      15.365  -2.018 -14.954  1.00  0.00\\nATOM    495  CB  ALA A  90       0.000   0.000   0.000  1.00  0.00\\nATOM    496  N   ALA A  91      13.132  -1.801 -14.880  1.00  0.00\\nATOM    497  CA  ALA A  91      13.204  -0.348 -14.778  1.00  0.00\\nATOM    498  C   ALA A  91      13.823   0.081 -13.454  1.00  0.00\\nATOM    499  O   ALA A  91      14.627   1.021 -13.403  1.00  0.00\\nATOM    500  CB  ALA A  91       0.000   0.000   0.000  1.00  0.00\\nATOM    501  N   ALA A  92      13.439  -0.613 -12.397  1.00  0.00\\nATOM    502  CA  ALA A  92      13.978  -0.269 -11.087  1.00  0.00\\nATOM    503  C   ALA A  92      15.452  -0.639 -10.983  1.00  0.00\\nATOM    504  O   ALA A  92      16.224   0.068 -10.323  1.00  0.00\\nATOM    505  CB  ALA A  92       0.000   0.000   0.000  1.00  0.00\\nATOM    506  N   ALA A  93      15.851  -1.747 -11.633  1.00  0.00\\nATOM    507  CA  ALA A  93      17.247  -2.167 -11.650  1.00  0.00\\nATOM    508  C   ALA A  93      18.129  -1.120 -12.318  1.00  0.00\\nATOM    509  O   ALA A  93      19.258  -0.852 -11.888  1.00  0.00\\nATOM    510  CB  ALA A  93       0.000   0.000   0.000  1.00  0.00\\nATOM    511  N   SER A  94      17.551  -0.519 -13.425  1.00  0.00\\nATOM    512  CA  SER A  94      18.283   0.526 -14.131  1.00  0.00\\nATOM    513  C   SER A  94      18.440   1.769 -13.265  1.00  0.00\\nATOM    514  O   SER A  94      19.499   2.409 -13.257  1.00  0.00\\nATOM    515  CB  SER A  94       0.000   0.000   0.000  1.00  0.00\\nATOM    516  OG  SER A  94       0.000   0.000   0.000  1.00  0.00\\nATOM    517  N   ALA A  95      17.366   2.100 -12.534  1.00  0.00\\nATOM    518  CA  ALA A  95      17.441   3.251 -11.643  1.00  0.00\\nATOM    519  C   ALA A  95      18.521   3.060 -10.586  1.00  0.00\\nATOM    520  O   ALA A  95      19.312   3.967 -10.296  1.00  0.00\\nATOM    521  CB  ALA A  95       0.000   0.000   0.000  1.00  0.00\\nATOM    522  N   ALA A  96      18.524   1.872 -10.033  1.00  0.00\\nATOM    523  CA  ALA A  96      19.513   1.579  -9.003  1.00  0.00\\nATOM    524  C   ALA A  96      20.926   1.612  -9.571  1.00  0.00\\nATOM    525  O   ALA A  96      21.851   2.104  -8.912  1.00  0.00\\nATOM    526  CB  ALA A  96       0.000   0.000   0.000  1.00  0.00\\nATOM    527  N   ALA A  97      21.094   1.096 -10.781  1.00  0.00\\nATOM    528  CA  ALA A  97      22.413   1.086 -11.402  1.00  0.00\\nATOM    529  C   ALA A  97      22.937   2.502 -11.604  1.00  0.00\\nATOM    530  O   ALA A  97      24.134   2.757 -11.421  1.00  0.00\\nATOM    531  CB  ALA A  97       0.000   0.000   0.000  1.00  0.00\\nATOM    532  N   ALA A  98      22.084   3.379 -11.963  1.00  0.00\\nATOM    533  CA  ALA A  98      22.521   4.750 -12.201  1.00  0.00\\nATOM    534  C   ALA A  98      22.876   5.449 -10.895  1.00  0.00\\nATOM    535  O   ALA A  98      23.679   6.391 -10.888  1.00  0.00\\nATOM    536  CB  ALA A  98       0.000   0.000   0.000  1.00  0.00\\nATOM    537  N   ALA A  99      22.266   4.982  -9.768  1.00  0.00\\nATOM    538  CA  ALA A  99      22.590   5.604  -8.490  1.00  0.00\\nATOM    539  C   ALA A  99      23.656   4.810  -7.745  1.00  0.00\\nATOM    540  O   ALA A  99      23.991   5.138  -6.600  1.00  0.00\\nATOM    541  CB  ALA A  99       0.000   0.000   0.000  1.00  0.00\\nATOM    542  N   SER A 100      24.136   3.869  -8.328  1.00  0.00\\nATOM    543  CA  SER A 100      25.226   3.036  -7.834  1.00  0.00\\nATOM    544  C   SER A 100      24.695   1.838  -7.056  1.00  0.00\\nATOM    545  O   SER A 100      23.828   1.962  -6.229  1.00  0.00\\nATOM    546  CB  SER A 100       0.000   0.000  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OQO B 347      -3.992  -2.556  -1.764  1.00  0.00           C\\nHETATM  560 C9   OQO B 347      -3.323  -1.716  -0.756  1.00  0.00           C\\nHETATM  561 C26  OQO B 347       3.754   2.272   0.494  1.00  0.00           C\\nHETATM  562 C33  OQO B 347       3.638   3.639   0.150  1.00  0.00           C\\nHETATM  563 C27  OQO B 347       5.041   1.731   0.564  1.00  0.00           C\\nHETATM  564 C29  OQO B 347       6.165   2.513   0.360  1.00  0.00           C\\nHETATM  565 C2   OQO B 347      -4.928  -2.088  -2.660  1.00  0.00           C\\nHETATM  566 C19  OQO B 347       0.532  -0.382   1.291  1.00  0.00           C\\nHETATM  567 C4   OQO B 347      -5.215  -4.204  -3.626  1.00  0.00           C\\nHETATM  568 C17  OQO B 347      -1.767  -4.259   2.637  1.00  0.00           C\\nHETATM  569 C18  OQO B 347      -2.012  -3.855   4.077  1.00  0.00           C\\nHETATM  570 C16  OQO B 347      -2.079  -2.810   2.972  1.00  0.00           C\\nHETATM  571 C1   OQO B 347      -5.349  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CB  ALA A   5       0.000   0.000   0.000  1.00  0.00\\nATOM     30  N   SER A   6      10.050 -14.239  -6.595  1.00  0.00\\nATOM     31  CA  SER A   6      11.406 -13.718  -6.724  1.00  0.00\\nATOM     32  C   SER A   6      11.419 -12.398  -7.484  1.00  0.00\\nATOM     33  O   SER A   6      12.221 -11.518  -7.146  1.00  0.00\\nATOM     34  CB  SER A   6       0.000   0.000   0.000  1.00  0.00\\nATOM     35  OG  SER A   6       0.000   0.000   0.000  1.00  0.00\\nATOM     36  N   ALA A   7      10.583 -12.225  -8.477  1.00  0.00\\nATOM     37  CA  ALA A   7      10.528 -10.987  -9.245  1.00  0.00\\nATOM     38  C   ALA A   7       9.984  -9.840  -8.403  1.00  0.00\\nATOM     39  O   ALA A   7      10.438  -8.694  -8.510  1.00  0.00\\nATOM     40  CB  ALA A   7       0.000   0.000   0.000  1.00  0.00\\nATOM     41  N   ALA A   8       8.993 -10.183  -7.556  1.00  0.00\\nATOM     42  CA  ALA A   8       8.436  -9.175  -6.661  1.00  0.00\\nATOM     43  C   ALA A   8       9.435  -8.788  -5.578  1.00  0.00\\nATOM     44  O   ALA A   8       9.547  -7.615  -5.199  1.00  0.00\\nATOM     45  CB  ALA A   8       0.000   0.000   0.000  1.00  0.00\\nATOM     46  N   ALA A   9      10.154  -9.800  -5.091  1.00  0.00\\nATOM     47  CA  ALA A   9      11.158  -9.552  -4.063  1.00  0.00\\nATOM     48  C   ALA A   9      12.273  -8.655  -4.586  1.00  0.00\\nATOM     49  O   ALA A   9      12.783  -7.797  -3.855  1.00  0.00\\nATOM     50  CB  ALA A   9       0.000   0.000   0.000  1.00  0.00\\nATOM     51  N   ALA A  10      12.654  -8.859  -5.876  1.00  0.00\\nATOM     52  CA  ALA A  10      13.679  -8.022  -6.488  1.00  0.00\\nATOM     53  C   ALA A  10      13.201  -6.583  -6.633  1.00  0.00\\nATOM     54  O   ALA A  10      13.954  -5.631  -6.390  1.00  0.00\\nATOM     55  CB  ALA A  10       0.000   0.000   0.000  1.00  0.00\\nATOM     56  N   ALA A  11      11.934  -6.447  -7.034  1.00  0.00\\nATOM     57  CA  ALA A  11      11.365  -5.109  -7.145  1.00  0.00\\nATOM     58  C   ALA A  11      11.366  -4.396  -5.799  1.00  0.00\\nATOM     59  O   ALA A  11      11.692  -3.205  -5.715  1.00  0.00\\nATOM     60  CB  ALA A  11       0.000   0.000   0.000  1.00  0.00\\nATOM     61  N   ALA A  12      11.003  -5.127  -4.759  1.00  0.00\\nATOM     62  CA  ALA A  12      10.951  -4.542  -3.425  1.00  0.00\\nATOM     63  C   ALA A  12      12.343  -4.163  -2.935  1.00  0.00\\nATOM     64  O   ALA A  12      12.505  -3.119  -2.290  1.00  0.00\\nATOM     65  CB  ALA A  12       0.000   0.000   0.000  1.00  0.00\\nATOM     66  N   ALA A  13      13.353  -4.995  -3.231  1.00  0.00\\nATOM     67  CA  ALA A  13      14.735  -4.718  -2.856  1.00  0.00\\nATOM     68  C   ALA A  13      15.237  -3.437  -3.511  1.00  0.00\\nATOM     69  O   ALA A  13      15.912  -2.604  -2.893  1.00  0.00\\nATOM     70  CB  ALA A  13       0.000   0.000   0.000  1.00  0.00\\nATOM     71  N   ALA A  14      14.854  -3.320  -4.856  1.00  0.00\\nATOM     72  CA  ALA A  14      15.279  -2.126  -5.577  1.00  0.00\\nATOM     73  C   ALA A  14      14.617  -0.876  -5.011  1.00  0.00\\nATOM     74  O   ALA A  14      15.278   0.153  -4.824  1.00  0.00\\nATOM     75  CB  ALA A  14       0.000   0.000   0.000  1.00  0.00\\nATOM     76  N   ALA A  15      13.319  -0.967  -4.742  1.00  0.00\\nATOM     77  CA  ALA A  15      12.595   0.173  -4.193  1.00  0.00\\nATOM     78  C   ALA A  15      13.185   0.609  -2.858  1.00  0.00\\nATOM     79  O   ALA A  15      13.365   1.809  -2.613  1.00  0.00\\nATOM     80  CB  ALA A  15       0.000   0.000   0.000  1.00  0.00\\nATOM     81  N   ALA A  16      13.479  -0.354  -2.009  1.00  0.00\\nATOM     82  CA  ALA A  16      13.991  -0.057  -0.676  1.00  0.00\\nATOM     83  C   ALA A  16      15.372   0.583  -0.746  1.00  0.00\\nATOM     84  O   ALA A  16      15.704   1.449   0.073  1.00  0.00\\nATOM     85  CB  ALA A  16       0.000   0.000   0.000  1.00  0.00\\nATOM     86  N   ALA A  17      16.188   0.146  -1.743  1.00  0.00\\nATOM     87  CA  ALA A  17      17.525   0.694  -1.934  1.00  0.00\\nATOM     88  C   ALA A  17      17.465   2.146  -2.389  1.00  0.00\\nATOM     89  O   ALA A  17      18.293   2.976  -1.991  1.00  0.00\\nATOM     90  CB  ALA A  17       0.000   0.000   0.000  1.00  0.00\\nATOM     91  N   ALA A  18      16.416   2.448  -3.277  1.00  0.00\\nATOM     92  CA  ALA A  18      16.229   3.822  -3.728  1.00  0.00\\nATOM     93  C   ALA A  18      15.765   4.718  -2.587  1.00  0.00\\nATOM     94  O   ALA A  18      16.191   5.876  -2.485  1.00  0.00\\nATOM     95  CB  ALA A  18       0.000   0.000   0.000  1.00  0.00\\nATOM     96  N   ALA A  19      14.895   4.183  -1.735  1.00  0.00\\nATOM     97  CA  ALA A  19      14.423   4.945  -0.585  1.00  0.00\\nATOM     98  C   ALA A  19      15.572   5.302   0.349  1.00  0.00\\nATOM     99  O   ALA A  19      15.617   6.409   0.901  1.00  0.00\\nATOM    100  CB  ALA A  19       0.000   0.000   0.000  1.00  0.00\\nATOM    101  N   ALA A  20      16.512   4.343   0.523  1.00  0.00\\nATOM    102  CA  ALA A  20      17.664   4.582   1.384  1.00  0.00\\nATOM    103  C   ALA A  20      18.585   5.640   0.790  1.00  0.00\\nATOM    104  O   ALA A  20      19.301   6.328   1.529  1.00  0.00\\nATOM    105  CB  ALA A  20       0.000   0.000   0.000  1.00  0.00\\nATOM    106  N   ALA A  21      18.572   5.772  -0.530  1.00  0.00\\nATOM    107  CA  ALA A  21      19.397   6.775  -1.193  1.00  0.00\\nATOM    108  C   ALA A  21      18.838   8.176  -0.981  1.00  0.00\\nATOM    109  O   ALA A  21      19.447   9.169  -1.401  1.00  0.00\\nATOM    110  CB  ALA A  21       0.000   0.000   0.000  1.00  0.00\\nATOM    111  N   LYS A  22      17.797   8.240  -0.396  1.00  0.00\\nATOM    112  CA  LYS A  22      17.262   9.557  -0.074  1.00  0.00\\nATOM    113  C   LYS A  22      16.186   9.972  -1.069  1.00  0.00\\nATOM    114  O   LYS A  22      15.790  11.143  -1.135  1.00  0.00\\nATOM    115  CB  LYS A  22       0.000   0.000   0.000  1.00  0.00\\nATOM    116  CG  LYS A  22       0.000   0.000   0.000  1.00  0.00\\nATOM    117  CD  LYS A  22       0.000   0.000   0.000  1.00  0.00\\nATOM    118  CE  LYS A  22       0.000   0.000   0.000  1.00  0.00\\nATOM    119  NZ  LYS A  22       0.000   0.000   0.000  1.00  0.00\\nATOM    120  N   ALA A  23      15.727   8.989  -1.836  1.00  0.00\\nATOM    121  CA  ALA A  23      14.687   9.324  -2.801  1.00  0.00\\nATOM    122  C   ALA A  23      13.312   9.342  -2.146  1.00  0.00\\nATOM    123  O   ALA A  23      13.072   8.519  -1.253  1.00  0.00\\nATOM    124  CB  ALA A  23       0.000   0.000   0.000  1.00  0.00\\nATOM    125  N   ALA A  24      12.476  10.152  -2.501  1.00  0.00\\nATOM    126  CA  ALA A  24      11.116  10.172  -1.976  1.00  0.00\\nATOM    127  C   ALA A  24      10.211   9.226  -2.755  1.00  0.00\\nATOM    128  O   ALA A  24      10.501   8.993  -3.936  1.00  0.00\\nATOM    129  CB  ALA A  24       0.000   0.000   0.000  1.00  0.00\\nATOM    130  N   ALA A  25       9.220   8.703  -2.237  1.00  0.00\\nATOM    131  CA  ALA A  25       8.333   7.766  -2.916  1.00  0.00\\nATOM    132  C   ALA A  25       7.762   8.373  -4.191  1.00  0.00\\nATOM    133  O   ALA A  25       7.574   7.655  -5.181  1.00  0.00\\nATOM    134  CB  ALA A  25       0.000   0.000   0.000  1.00  0.00\\nATOM    135  N   ALA A  26       7.488   9.655  -4.188  1.00  0.00\\nATOM    136  CA  ALA A  26       6.917  10.326  -5.349  1.00  0.00\\nATOM    137  C   ALA A  26       7.919  10.393  -6.495  1.00  0.00\\nATOM    138  O   ALA A  26       7.580  10.172  -7.664  1.00  0.00\\nATOM    139  CB  ALA A  26       0.000   0.000   0.000  1.00  0.00\\nATOM    140  N   ALA A  27       9.191  10.714  -6.109  1.00  0.00\\nATOM    141  CA  ALA A  27      10.256  10.724  -7.104  1.00  0.00\\nATOM    142  C   ALA A  27      10.514   9.325  -7.649  1.00  0.00\\nATOM    143  O   ALA A  27      10.777   9.152  -8.846  1.00  0.00\\nATOM    144  CB  ALA A  27       0.000   0.000   0.000  1.00  0.00\\nATOM    145  N   ALA A  28      10.437   8.337  -6.765  1.00  0.00\\nATOM    146  CA  ALA A  28      10.623   6.956  -7.193  1.00  0.00\\nATOM    147  C   ALA A  28       9.574   6.552  -8.221  1.00  0.00\\nATOM    148  O   ALA A  28       9.910   5.972  -9.261  1.00  0.00\\nATOM    149  CB  ALA A  28       0.000   0.000   0.000  1.00  0.00\\nATOM    150  N   ALA A  29       8.312   6.855  -7.935  1.00  0.00\\nATOM    151  CA  ALA A  29       7.205   6.463  -8.799  1.00  0.00\\nATOM    152  C   ALA A  29       7.286   7.162 -10.150  1.00  0.00\\nATOM    153  O   ALA A  29       7.039   6.556 -11.200  1.00  0.00\\nATOM    154  CB  ALA A  29       0.000   0.000   0.000  1.00  0.00\\nATOM    155  N   ALA A  30       7.648   8.488 -10.096  1.00  0.00\\nATOM    156  CA  ALA A  30       7.804   9.252 -11.328  1.00  0.00\\nATOM    157  C   ALA A  30       8.917   8.678 -12.195  1.00  0.00\\nATOM    158  O   ALA A  30       8.751   8.559 -13.416  1.00  0.00\\nATOM    159  CB  ALA A  30       0.000   0.000   0.000  1.00  0.00\\nATOM    160  N   SER A  31      10.013   8.333 -11.602  1.00  0.00\\nATOM    161  CA  SER A  31      11.146   7.829 -12.369  1.00  0.00\\nATOM    162  C   SER A  31      10.871   6.429 -12.902  1.00  0.00\\nATOM    163  O   SER A  31      11.287   6.073 -14.011  1.00  0.00\\nATOM    164  CB  SER A  31       0.000   0.000   0.000  1.00  0.00\\nATOM    165  OG  SER A  31       0.000   0.000   0.000  1.00  0.00\\nATOM    166  N   ALA A  32      10.149   5.630 -12.072  1.00  0.00\\nATOM    167  CA  ALA A  32       9.783   4.283 -12.493  1.00  0.00\\nATOM    168  C   ALA A  32       8.824   4.317 -13.676  1.00  0.00\\nATOM    169  O   ALA A  32       8.935   3.516 -14.613  1.00  0.00\\nATOM    170  CB  ALA A  32       0.000   0.000   0.000  1.00  0.00\\nATOM    171  N   ALA A  33       7.858   5.285 -13.609  1.00  0.00\\nATOM    172  CA  ALA A  33       6.892   5.443 -14.690  1.00  0.00\\nATOM    173  C   ALA A  33       7.582   5.822 -15.994  1.00  0.00\\nATOM    174  O   ALA A  33       7.255   5.291 -17.063  1.00  0.00\\nATOM    175  CB  ALA A  33       0.000   0.000   0.000  1.00  0.00\\nATOM    176  N   SER A  34       8.548   6.755 -15.889  1.00  0.00\\nATOM    177  CA  SER A  34       9.239   7.212 -17.089  1.00  0.00\\nATOM    178  C   SER A  34      10.080   6.098 -17.698  1.00  0.00\\nATOM    179  O   SER A  34      10.188   5.995 -18.927  1.00  0.00\\nATOM    180  CB  SER A  34       0.000   0.000   0.000  1.00  0.00\\nATOM    181  OG  SER A  34       0.000   0.000   0.000  1.00  0.00\\nATOM    182  N   SER A  35      10.683   5.255 -16.831  1.00  0.00\\nATOM    183  CA  SER A  35      11.503   4.152 -17.318  1.00  0.00\\nATOM    184  C   SER A  35      10.643   3.061 -17.943  1.00  0.00\\nATOM    185  O   SER A  35      11.025   2.449 -18.949  1.00  0.00\\nATOM    186  CB  SER A  35       0.000   0.000   0.000  1.00  0.00\\nATOM    187  OG  SER A  35       0.000   0.000   0.000  1.00  0.00\\nATOM    188  N   ALA A  36       9.486   2.828 -17.336  1.00  0.00\\nATOM    189  CA  ALA A  36       8.533   1.860 -17.865  1.00  0.00\\nATOM    190  C   ALA A  36       7.954   2.327 -19.195  1.00  0.00\\nATOM    191  O   ALA A  36       7.715   1.521 -20.103  1.00  0.00\\nATOM    192  CB  ALA A  36       0.000   0.000   0.000  1.00  0.00\\nATOM    193  N   ALA A  37       7.727   3.689 -19.294  1.00  0.00\\nATOM    194  CA  ALA A  37       7.200   4.262 -20.527  1.00  0.00\\nATOM    195  C   ALA A  37       8.176   4.077 -21.682  1.00  0.00\\nATOM    196  O   ALA A  37       7.776   3.954 -22.846  1.00  0.00\\nATOM    197  CB  ALA A  37       0.000   0.000   0.000  1.00  0.00\\nATOM    198  N   SER A  38       9.495   4.060 -21.322  1.00  0.00\\nATOM    199  CA  SER A  38      10.520   3.837 -22.335  1.00  0.00\\nATOM    200  C   SER A  38      10.499   2.397 -22.832  1.00  0.00\\nATOM    201  O   SER A  38      10.849   2.117 -23.986  1.00  0.00\\nATOM    202  CB  SER A  38       0.000   0.000   0.000  1.00  0.00\\nATOM    203  OG  SER A  38       0.000   0.000   0.000  1.00  0.00\\nATOM    204  N   ALA A  39      10.074   1.474 -21.927  1.00  0.00\\nATOM    205  CA  ALA A  39       9.960   0.069 -22.299  1.00  0.00\\nATOM    206  C   ALA A  39       8.594  -0.233 -22.901  1.00  0.00\\nATOM    207  O   ALA A  39       8.526  -1.027 -23.848  1.00  0.00\\nATOM    208  CB  ALA A  39       0.000   0.000   0.000  1.00  0.00\\nATOM    209  N   ALA A  40       7.469   0.373 -22.393  1.00  0.00\\nATOM    210  CA  ALA A  40       6.105   0.225 -22.885  1.00  0.00\\nATOM    211  C   ALA A  40       5.400   1.573 -22.967  1.00  0.00\\nATOM    212  O   ALA A  40       4.981   2.067 -21.912  1.00  0.00\\nATOM    213  CB  ALA A  40       0.000   0.000   0.000  1.00  0.00\\nATOM    214  N   GLN A  41       5.246   2.155 -24.028  1.00  0.00\\nATOM    215  CA  GLN A  41       4.757   3.512 -24.243  1.00  0.00\\nATOM    216  C   GLN A  41       3.398   3.719 -23.586  1.00  0.00\\nATOM    217  O   GLN A  41       3.171   4.931 -23.484  1.00  0.00\\nATOM    218  CB  GLN A  41       0.000   0.000   0.000  1.00  0.00\\nATOM    219  CG  GLN A  41       0.000   0.000   0.000  1.00  0.00\\nATOM    220  CD  GLN A  41       0.000   0.000   0.000  1.00  0.00\\nATOM    221  OE1 GLN A  41       0.000   0.000   0.000  1.00  0.00\\nATOM    222  NE2 GLN A  41       0.000   0.000   0.000  1.00  0.00\\nATOM    223  N   GLN A  42       2.654   3.162 -23.222  1.00  0.00\\nATOM    224  CA  GLN A  42       1.297   3.321 -22.712  1.00  0.00\\nATOM    225  C   GLN A  42       1.271   3.269 -21.190  1.00  0.00\\nATOM    226  O   GLN A  42       0.173   3.347 -20.624  1.00  0.00\\nATOM    227  CB  GLN A  42       0.000   0.000   0.000  1.00  0.00\\nATOM    228  CG  GLN A  42       0.000   0.000   0.000  1.00  0.00\\nATOM    229  CD  GLN A  42       0.000   0.000   0.000  1.00  0.00\\nATOM    230  OE1 GLN A  42       0.000   0.000   0.000  1.00  0.00\\nATOM    231  NE2 GLN A  42       0.000   0.000   0.000  1.00  0.00\\nATOM    232  N   ALA A  43       2.377   3.145 -20.497  1.00  0.00\\nATOM    233  CA  ALA A  43       2.437   3.045 -19.044  1.00  0.00\\nATOM    234  C   ALA A  43       2.344   4.419 -18.393  1.00  0.00\\nATOM    235  O   ALA A  43       3.021   5.351 -18.844  1.00  0.00\\nATOM    236  CB  ALA A  43       0.000   0.000   0.000  1.00  0.00\\nATOM    237  N   ALA A  44       1.598   4.561 -17.437  1.00  0.00\\nATOM    238  CA  ALA A  44       1.430   5.818 -16.718  1.00  0.00\\nATOM    239  C   ALA A  44       1.658   5.632 -15.223  1.00  0.00\\nATOM    240  O   ALA A  44       1.819   4.489 -14.779  1.00  0.00\\nATOM    241  CB  ALA A  44       0.000   0.000   0.000  1.00  0.00\\nATOM    242  N   SER A  45       1.678   6.687 -14.444  1.00  0.00\\nATOM    243  CA  SER A  45       1.838   6.643 -12.995  1.00  0.00\\nATOM    244  C   SER A  45       0.729   5.828 -12.343  1.00  0.00\\nATOM    245  O   SER A  45       0.991   5.098 -11.378  1.00  0.00\\nATOM    246  CB  SER A  45       0.000   0.000   0.000  1.00  0.00\\nATOM    247  OG  SER A  45       0.000   0.000   0.000  1.00  0.00\\nATOM    248  N   ALA A  46      -0.515   5.937 -12.850  1.00  0.00\\nATOM    249  CA  ALA A  46      -1.649   5.185 -12.325  1.00  0.00\\nATOM    250  C   ALA A  46      -1.395   3.685 -12.395  1.00  0.00\\nATOM    251  O   ALA A  46      -1.635   2.939 -11.436  1.00  0.00\\nATOM    252  CB  ALA A  46       0.000   0.000   0.000  1.00  0.00\\nATOM    253  N   ALA A  47      -0.894   3.265 -13.586  1.00  0.00\\nATOM    254  CA  ALA A  47      -0.618   1.843 -13.749  1.00  0.00\\nATOM    255  C   ALA A  47       0.448   1.373 -12.768  1.00  0.00\\nATOM    256  O   ALA A  47       0.349   0.274 -12.208  1.00  0.00\\nATOM    257  CB  ALA A  47       0.000   0.000   0.000  1.00  0.00\\nATOM    258  N   ALA A  48       1.466   2.211 -12.566  1.00  0.00\\nATOM    259  CA  ALA A  48       2.554   1.854 -11.663  1.00  0.00\\nATOM    260  C   ALA A  48       2.073   1.790 -10.219  1.00  0.00\\nATOM    261  O   ALA A  48       2.473   0.867  -9.498  1.00  0.00\\nATOM    262  CB  ALA A  48       0.000   0.000   0.000  1.00  0.00\\nATOM    263  N   ALA A  49       1.298   2.652  -9.797  1.00  0.00\\nATOM    264  CA  ALA A  49       0.764   2.669  -8.440  1.00  0.00\\nATOM    265  C   ALA A  49      -0.063   1.421  -8.158  1.00  0.00\\nATOM    266  O   ALA A  49       0.063   0.793  -7.099  1.00  0.00\\nATOM    267  CB  ALA A  49       0.000   0.000   0.000  1.00  0.00\\nATOM    268  N   SER A  50      -0.927   1.074  -9.152  1.00  0.00\\nATOM    269  CA  SER A  50      -1.738  -0.129  -9.006  1.00  0.00\\nATOM    270  C   SER A  50      -0.867  -1.377  -8.950  1.00  0.00\\nATOM    271  O   SER A  50      -1.131  -2.299  -8.168  1.00  0.00\\nATOM    272  CB  SER A  50       0.000   0.000   0.000  1.00  0.00\\nATOM    273  OG  SER A  50       0.000   0.000   0.000  1.00  0.00\\nATOM    274  N   ALA A  51       0.133  -1.395  -9.756  1.00  0.00\\nATOM    275  CA  ALA A  51       1.016  -2.555  -9.800  1.00  0.00\\nATOM    276  C   ALA A  51       1.736  -2.750  -8.472  1.00  0.00\\nATOM    277  O   ALA A  51       1.887  -3.879  -7.988  1.00  0.00\\nATOM    278  CB  ALA A  51       0.000   0.000   0.000  1.00  0.00\\nATOM    279  N   ALA A  52       2.172  -1.641  -7.901  1.00  0.00\\nATOM    280  CA  ALA A  52       2.899  -1.694  -6.638  1.00  0.00\\nATOM    281  C   ALA A  52       1.992  -2.140  -5.498  1.00  0.00\\nATOM    282  O   ALA A  52       2.410  -2.929  -4.642  1.00  0.00\\nATOM    283  CB  ALA A  52       0.000   0.000   0.000  1.00  0.00\\nATOM    284  N   ALA A  53       0.788  -1.654  -5.484  1.00  0.00\\nATOM    285  CA  ALA A  53      -0.163  -2.012  -4.438  1.00  0.00\\nATOM    286  C   ALA A  53      -0.545  -3.484  -4.522  1.00  0.00\\nATOM    287  O   ALA A  53      -0.626  -4.184  -3.504  1.00  0.00\\nATOM    288  CB  ALA A  53       0.000   0.000   0.000  1.00  0.00\\nATOM    289  N   ALA A  54      -0.779  -3.939  -5.765  1.00  0.00\\nATOM    290  CA  ALA A  54      -1.161  -5.334  -5.950  1.00  0.00\\nATOM    291  C   ALA A  54      -0.010  -6.271  -5.607  1.00  0.00\\nATOM    292  O   ALA A  54      -0.211  -7.328  -4.996  1.00  0.00\\nATOM    293  CB  ALA A  54       0.000   0.000   0.000  1.00  0.00\\nATOM    294  N   ALA A  55       1.202  -5.866  -6.011  1.00  0.00\\nATOM    295  CA  ALA A  55       2.379  -6.687  -5.752  1.00  0.00\\nATOM    296  C   ALA A  55       2.667  -6.782  -4.259  1.00  0.00\\nATOM    297  O   ALA A  55       3.067  -7.839  -3.755  1.00  0.00\\nATOM    298  CB  ALA A  55       0.000   0.000   0.000  1.00  0.00\\nATOM    299  N   ALA A  56       2.455  -5.648  -3.555  1.00  0.00\\nATOM    300  CA  ALA A  56       2.642  -5.611  -2.110  1.00  0.00\\nATOM    301  C   ALA A  56       1.676  -6.555  -1.405  1.00  0.00\\nATOM    302  O   ALA A  56       2.034  -7.258  -0.451  1.00  0.00\\nATOM    303  CB  ALA A  56       0.000   0.000   0.000  1.00  0.00\\nATOM    304  N   ALA A  57       0.418  -6.540  -1.920  1.00  0.00\\nATOM    305  CA  ALA A  57      -0.594  -7.425  -1.356  1.00  0.00\\nATOM    306  C   ALA A  57      -0.269  -8.886  -1.641  1.00  0.00\\nATOM    307  O   ALA A  57      -0.441  -9.749  -0.771  1.00  0.00\\nATOM    308  CB  ALA A  57       0.000   0.000   0.000  1.00  0.00\\nATOM    309  N   ALA A  58       0.214  -9.165  -2.898  1.00  0.00\\nATOM    310  CA  ALA A  58       0.567 -10.532  -3.261  1.00  0.00\\nATOM    311  C   ALA A  58       1.700 -11.059  -2.389  1.00  0.00\\nATOM    312  O   ALA A  58       1.666 -12.219  -1.961  1.00  0.00\\nATOM    313  CB  ALA A  58       0.000   0.000   0.000  1.00  0.00\\nATOM    314  N   SER A  59       2.705 -10.213  -2.124  1.00  0.00\\nATOM    315  CA  SER A  59       3.822 -10.611  -1.276  1.00  0.00\\nATOM    316  C   SER A  59       3.361 -10.889   0.149  1.00  0.00\\nATOM    317  O   SER A  59       3.839 -11.829   0.796  1.00  0.00\\nATOM    318  CB  SER A  59       0.000   0.000   0.000  1.00  0.00\\nATOM    319  OG  SER A  59       0.000   0.000   0.000  1.00  0.00\\nATOM    320  N   ALA A  60       2.409 -10.045   0.641  1.00  0.00\\nATOM    321  CA  ALA A  60       1.841 -10.253   1.968  1.00  0.00\\nATOM    322  C   ALA A  60       1.130 -11.597   2.058  1.00  0.00\\nATOM    323  O   ALA A  60       1.230 -12.288   3.080  1.00  0.00\\nATOM    324  CB  ALA A  60       0.000   0.000   0.000  1.00  0.00\\nATOM    325  N   SER A  61       0.402 -11.974   0.981  1.00  0.00\\nATOM    326  CA  SER A  61      -0.301 -13.251   0.959  1.00  0.00\\nATOM    327  C   SER A  61       0.677 -14.419   0.954  1.00  0.00\\nATOM    328  O   SER A  61       0.435 -15.444   1.604  1.00  0.00\\nATOM    329  CB  SER A  61       0.000   0.000   0.000  1.00  0.00\\nATOM    330  OG  SER A  61       0.000   0.000   0.000  1.00  0.00\\nATOM    331  N   ALA A  62       1.771 -14.260   0.226  1.00  0.00\\nATOM    332  CA  ALA A  62       2.791 -15.300   0.162  1.00  0.00\\nATOM    333  C   ALA A  62       3.410 -15.550   1.531  1.00  0.00\\nATOM    334  O   ALA A  62       3.666 -16.695   1.925  1.00  0.00\\nATOM    335  CB  ALA A  62       0.000   0.000   0.000  1.00  0.00\\nATOM    336  N   ALA A  63       3.648 -14.409   2.263  1.00  0.00\\nATOM    337  CA  ALA A  63       4.248 -14.473   3.590  1.00  0.00\\nATOM    338  C   ALA A  63       3.319 -15.162   4.581  1.00  0.00\\nATOM    339  O   ALA A  63       3.763 -15.854   5.506  1.00  0.00\\nATOM    340  CB  ALA A  63       0.000   0.000   0.000  1.00  0.00\\nATOM    341  N   ALA A  64       1.983 -14.947   4.354  1.00  0.00\\nATOM    342  CA  ALA A  64       0.995 -15.590   5.212  1.00  0.00\\nATOM    343  C   ALA A  64       0.839 -17.065   4.863  1.00  0.00\\nATOM    344  O   ALA A  64       0.005 -17.733   5.486  1.00  0.00\\nATOM    345  CB  ALA A  64       0.000   0.000   0.000  1.00  0.00\\nATOM    346  N   LYS A  65       1.522 -17.561   3.994  1.00  0.00\\nATOM    347  CA  LYS A  65       1.524 -19.005   3.794  1.00  0.00\\nATOM    348  C   LYS A  65       0.648 -19.399   2.611  1.00  0.00\\nATOM    349  O   LYS A  65       0.324 -20.583   2.459  1.00  0.00\\nATOM    350  CB  LYS A  65       0.000   0.000   0.000  1.00  0.00\\nATOM    351  CG  LYS A  65       0.000   0.000   0.000  1.00  0.00\\nATOM    352  CD  LYS A  65       0.000   0.000   0.000  1.00  0.00\\nATOM    353  CE  LYS A  65       0.000   0.000   0.000  1.00  0.00\\nATOM    354  NZ  LYS A  65       0.000   0.000   0.000  1.00  0.00\\nATOM    355  N   ALA A  66       0.281 -18.495   1.822  1.00  0.00\\nATOM    356  CA  ALA A  66      -0.598 -18.850   0.714  1.00  0.00\\nATOM    357  C   ALA A  66       0.187 -19.466  -0.437  1.00  0.00\\nATOM    358  O   ALA A  66       1.317 -19.037  -0.706  1.00  0.00\\nATOM    359  CB  ALA A  66       0.000   0.000   0.000  1.00  0.00\\nATOM    360  N   SER A  67      -0.365 -20.430  -1.101  1.00  0.00\\nATOM    361  CA  SER A  67       0.323 -20.968  -2.268  1.00  0.00\\nATOM    362  C   SER A  67       0.422 -19.929  -3.377  1.00  0.00\\nATOM    363  O   SER A  67      -0.538 -19.164  -3.534  1.00  0.00\\nATOM    364  CB  SER A  67       0.000   0.000   0.000  1.00  0.00\\nATOM    365  OG  SER A  67       0.000   0.000   0.000  1.00  0.00\\nATOM    366  N   ALA A  68       1.439 -19.838  -4.118  1.00  0.00\\nATOM    367  CA  ALA A  68       1.627 -18.871  -5.193  1.00  0.00\\nATOM    368  C   ALA A  68       0.548 -19.015  -6.259  1.00  0.00\\nATOM    369  O   ALA A  68       0.095 -18.032  -6.859  1.00  0.00\\nATOM    370  CB  ALA A  68       0.000   0.000   0.000  1.00  0.00\\nATOM    371  N   SER A  69       0.146 -20.304  -6.477  1.00  0.00\\nATOM    372  CA  SER A  69      -0.918 -20.531  -7.447  1.00  0.00\\nATOM    373  C   SER A  69      -2.234 -19.928  -6.972  1.00  0.00\\nATOM    374  O   SER A  69      -2.983 -19.383  -7.793  1.00  0.00\\nATOM    375  CB  SER A  69       0.000   0.000   0.000  1.00  0.00\\nATOM    376  OG  SER A  69       0.000   0.000   0.000  1.00  0.00\\nATOM    377  N   ALA A  70      -2.531 -20.007  -5.709  1.00  0.00\\nATOM    378  CA  ALA A  70      -3.734 -19.412  -5.140  1.00  0.00\\nATOM    379  C   ALA A  70      -3.695 -17.892  -5.235  1.00  0.00\\nATOM    380  O   ALA A  70      -4.706 -17.231  -5.502  1.00  0.00\\nATOM    381  CB  ALA A  70       0.000   0.000   0.000  1.00  0.00\\nATOM    382  N   ALA A  71      -2.417 -17.335  -4.993  1.00  0.00\\nATOM    383  CA  ALA A  71      -2.210 -15.895  -5.094  1.00  0.00\\nATOM    384  C   ALA A  71      -2.460 -15.401  -6.513  1.00  0.00\\nATOM    385  O   ALA A  71      -3.092 -14.356  -6.712  1.00  0.00\\nATOM    386  CB  ALA A  71       0.000   0.000   0.000  1.00  0.00\\nATOM    387  N   ALA A  72      -1.952 -16.168  -7.516  1.00  0.00\\nATOM    388  CA  ALA A  72      -2.109 -15.791  -8.916  1.00  0.00\\nATOM    389  C   ALA A  72      -3.567 -15.879  -9.350  1.00  0.00\\nATOM    390  O   ALA A  72      -4.057 -15.053 -10.130  1.00  0.00\\nATOM    391  CB  ALA A  72       0.000   0.000   0.000  1.00  0.00\\nATOM    392  N   LYS A  73      -4.244 -16.907  -8.823  1.00  0.00\\nATOM    393  CA  LYS A  73      -5.656 -17.062  -9.152  1.00  0.00\\nATOM    394  C   LYS A  73      -6.493 -15.953  -8.528  1.00  0.00\\nATOM    395  O   LYS A  73      -7.479 -15.513  -9.132  1.00  0.00\\nATOM    396  CB  LYS A  73       0.000   0.000   0.000  1.00  0.00\\nATOM    397  CG  LYS A  73       0.000   0.000   0.000  1.00  0.00\\nATOM    398  CD  LYS A  73       0.000   0.000   0.000  1.00  0.00\\nATOM    399  CE  LYS A  73       0.000   0.000   0.000  1.00  0.00\\nATOM    400  NZ  LYS A  73       0.000   0.000   0.000  1.00  0.00\\nATOM    401  N   ALA A  74      -6.118 -15.493  -7.332  1.00  0.00\\nATOM    402  CA  ALA A  74      -6.868 -14.436  -6.664  1.00  0.00\\nATOM    403  C   ALA A  74      -6.591 -13.079  -7.298  1.00  0.00\\nATOM    404  O   ALA A  74      -7.447 -12.186  -7.279  1.00  0.00\\nATOM    405  CB  ALA A  74       0.000   0.000   0.000  1.00  0.00\\nATOM    406  N   ALA A  75      -5.347 -12.929  -7.877  1.00  0.00\\nATOM    407  CA  ALA A  75      -5.006 -11.661  -8.510  1.00  0.00\\nATOM    408  C   ALA A  75      -4.968 -11.795 -10.027  1.00  0.00\\nATOM    409  O   ALA A  75      -3.952 -11.465 -10.651  1.00  0.00\\nATOM    410  CB  ALA A  75       0.000   0.000   0.000  1.00  0.00\\nATOM    411  N   GLN A  76      -6.034 -12.264 -10.612  1.00  0.00\\nATOM    412  CA  GLN A  76      -6.165 -12.674 -12.005  1.00  0.00\\nATOM    413  C   GLN A  76      -5.661 -11.589 -12.948  1.00  0.00\\nATOM    414  O   GLN A  76      -4.893 -11.919 -13.860  1.00  0.00\\nATOM    415  CB  GLN A  76       0.000   0.000   0.000  1.00  0.00\\nATOM    416  CG  GLN A  76       0.000   0.000   0.000  1.00  0.00\\nATOM    417  CD  GLN A  76       0.000   0.000   0.000  1.00  0.00\\nATOM    418  OE1 GLN A  76       0.000   0.000   0.000  1.00  0.00\\nATOM    419  NE2 GLN A  76       0.000   0.000   0.000  1.00  0.00\\nATOM    420  N   ALA A  77      -6.028 -10.357 -12.799  1.00  0.00\\nATOM    421  CA  ALA A  77      -5.621  -9.295 -13.712  1.00  0.00\\nATOM    422  C   ALA A  77      -4.112  -9.091 -13.681  1.00  0.00\\nATOM    423  O   ALA A  77      -3.452  -8.816 -14.692  1.00  0.00\\nATOM    424  CB  ALA A  77       0.000   0.000   0.000  1.00  0.00\\nATOM    425  N   ALA A  78      -3.583  -9.252 -12.386  1.00  0.00\\nATOM    426  CA  ALA A  78      -2.146  -9.065 -12.223  1.00  0.00\\nATOM    427  C   ALA A  78      -1.365 -10.190 -12.891  1.00  0.00\\nATOM    428  O   ALA A  78      -0.274 -10.010 -13.448  1.00  0.00\\nATOM    429  CB  ALA A  78       0.000   0.000   0.000  1.00  0.00\\nATOM    430  N   ALA A  79      -2.033 -11.426 -12.791  1.00  0.00\\nATOM    431  CA  ALA A  79      -1.377 -12.610 -13.332  1.00  0.00\\nATOM    432  C   ALA A  79      -1.391 -12.599 -14.855  1.00  0.00\\nATOM    433  O   ALA A  79      -0.501 -13.205 -15.466  1.00  0.00\\nATOM    434  CB  ALA A  79       0.000   0.000   0.000  1.00  0.00\\nATOM    435  N   LYS A  80      -2.310 -11.973 -15.464  1.00  0.00\\nATOM    436  CA  LYS A  80      -2.421 -11.900 -16.916  1.00  0.00\\nATOM    437  C   LYS A  80      -1.389 -10.943 -17.500  1.00  0.00\\nATOM    438  O   LYS A  80      -0.977 -11.055 -18.661  1.00  0.00\\nATOM    439  CB  LYS A  80       0.000   0.000   0.000  1.00  0.00\\nATOM    440  CG  LYS A  80       0.000   0.000   0.000  1.00  0.00\\nATOM    441  CD  LYS A  80       0.000   0.000   0.000  1.00  0.00\\nATOM    442  CE  LYS A  80       0.000   0.000   0.000  1.00  0.00\\nATOM    443  NZ  LYS A  80       0.000   0.000   0.000  1.00  0.00\\nATOM    444  N   ALA A  81      -0.962  -9.922 -16.573  1.00  0.00\\nATOM    445  CA  ALA A  81      -0.047  -8.891 -17.048  1.00  0.00\\nATOM    446  C   ALA A  81       1.318  -9.018 -16.385  1.00  0.00\\nATOM    447  O   ALA A  81       1.992  -7.999 -16.188  1.00  0.00\\nATOM    448  CB  ALA A  81       0.000   0.000   0.000  1.00  0.00\\nATOM    449  N   ALA A  82       1.737 -10.195 -16.044  1.00  0.00\\nATOM    450  CA  ALA A  82       2.977 -10.476 -15.330  1.00  0.00\\nATOM    451  C   ALA A  82       4.177  -9.881 -16.055  1.00  0.00\\nATOM    452  O   ALA A  82       5.219  -9.681 -15.418  1.00  0.00\\nATOM    453  CB  ALA A  82       0.000   0.000   0.000  1.00  0.00\\nATOM    454  N   ALA A  83       4.084  -9.588 -17.350  1.00  0.00\\nATOM    455  CA  ALA A  83       5.130  -8.945 -18.136  1.00  0.00\\nATOM    456  C   ALA A  83       5.384  -7.522 -17.655  1.00  0.00\\nATOM    457  O   ALA A  83       6.488  -6.975 -17.778  1.00  0.00\\nATOM    458  CB  ALA A  83       0.000   0.000   0.000  1.00  0.00\\nATOM    459  N   ALA A  84       4.283  -6.937 -17.091  1.00  0.00\\nATOM    460  CA  ALA A  84       4.442  -5.589 -16.558  1.00  0.00\\nATOM    461  C   ALA A  84       5.333  -5.586 -15.323  1.00  0.00\\nATOM    462  O   ALA A  84       6.089  -4.645 -15.050  1.00  0.00\\nATOM    463  CB  ALA A  84       0.000   0.000   0.000  1.00  0.00\\nATOM    464  N   ALA A  85       5.193  -6.730 -14.571  1.00  0.00\\nATOM    465  CA  ALA A  85       6.009  -6.876 -13.372  1.00  0.00\\nATOM    466  C   ALA A  85       7.485  -7.010 -13.723  1.00  0.00\\nATOM    467  O   ALA A  85       8.351  -6.494 -13.005  1.00  0.00\\nATOM    468  CB  ALA A  85       0.000   0.000   0.000  1.00  0.00\\nATOM    469  N   ALA A  86       7.766  -7.702 -14.824  1.00  0.00\\nATOM    470  CA  ALA A  86       9.128  -7.901 -15.304  1.00  0.00\\nATOM    471  C   ALA A  86       9.762  -6.582 -15.727  1.00  0.00\\nATOM    472  O   ALA A  86      10.937  -6.309 -15.451  1.00  0.00\\nATOM    473  CB  ALA A  86       0.000   0.000   0.000  1.00  0.00\\nATOM    474  N   SER A  87       8.933  -5.767 -16.412  1.00  0.00\\nATOM    475  CA  SER A  87       9.417  -4.478 -16.892  1.00  0.00\\nATOM    476  C   SER A  87       9.705  -3.532 -15.733  1.00  0.00\\nATOM    477  O   SER A  87      10.679  -2.768 -15.735  1.00  0.00\\nATOM    478  CB  SER A  87       0.000   0.000   0.000  1.00  0.00\\nATOM    479  OG  SER A  87       0.000   0.000   0.000  1.00  0.00\\nATOM    480  N   ALA A  88       8.792  -3.623 -14.727  1.00  0.00\\nATOM    481  CA  ALA A  88       8.950  -2.776 -13.551  1.00  0.00\\nATOM    482  C   ALA A  88      10.245  -3.092 -12.814  1.00  0.00\\nATOM    483  O   ALA A  88      10.957  -2.192 -12.350  1.00  0.00\\nATOM    484  CB  ALA A  88       0.000   0.000   0.000  1.00  0.00\\nATOM    485  N   SER A  89      10.531  -4.406 -12.717  1.00  0.00\\nATOM    486  CA  SER A  89      11.750  -4.813 -12.029  1.00  0.00\\nATOM    487  C   SER A  89      12.990  -4.376 -12.799  1.00  0.00\\nATOM    488  O   SER A  89      14.012  -4.016 -12.201  1.00  0.00\\nATOM    489  CB  SER A  89       0.000   0.000   0.000  1.00  0.00\\nATOM    490  OG  SER A  89       0.000   0.000   0.000  1.00  0.00\\nATOM    491  N   ALA A  90      12.884  -4.414 -14.179  1.00  0.00\\nATOM    492  CA  ALA A  90      13.996  -4.005 -15.029  1.00  0.00\\nATOM    493  C   ALA A  90      14.226  -2.501 -14.950  1.00  0.00\\nATOM    494  O   ALA A  90      15.365  -2.018 -14.954  1.00  0.00\\nATOM    495  CB  ALA A  90       0.000   0.000   0.000  1.00  0.00\\nATOM    496  N   ALA A  91      13.132  -1.801 -14.880  1.00  0.00\\nATOM    497  CA  ALA A  91      13.204  -0.348 -14.778  1.00  0.00\\nATOM    498  C   ALA A  91      13.823   0.081 -13.454  1.00  0.00\\nATOM    499  O   ALA A  91      14.627   1.021 -13.403  1.00  0.00\\nATOM    500  CB  ALA A  91       0.000   0.000   0.000  1.00  0.00\\nATOM    501  N   ALA A  92      13.439  -0.613 -12.397  1.00  0.00\\nATOM    502  CA  ALA A  92      13.978  -0.269 -11.087  1.00  0.00\\nATOM    503  C   ALA A  92      15.452  -0.639 -10.983  1.00  0.00\\nATOM    504  O   ALA A  92      16.224   0.068 -10.323  1.00  0.00\\nATOM    505  CB  ALA A  92       0.000   0.000   0.000  1.00  0.00\\nATOM    506  N   ALA A  93      15.851  -1.747 -11.633  1.00  0.00\\nATOM    507  CA  ALA A  93      17.247  -2.167 -11.650  1.00  0.00\\nATOM    508  C   ALA A  93      18.129  -1.120 -12.318  1.00  0.00\\nATOM    509  O   ALA A  93      19.258  -0.852 -11.888  1.00  0.00\\nATOM    510  CB  ALA A  93       0.000   0.000   0.000  1.00  0.00\\nATOM    511  N   SER A  94      17.551  -0.519 -13.425  1.00  0.00\\nATOM    512  CA  SER A  94      18.283   0.526 -14.131  1.00  0.00\\nATOM    513  C   SER A  94      18.440   1.769 -13.265  1.00  0.00\\nATOM    514  O   SER A  94      19.499   2.409 -13.257  1.00  0.00\\nATOM    515  CB  SER A  94       0.000   0.000   0.000  1.00  0.00\\nATOM    516  OG  SER A  94       0.000   0.000   0.000  1.00  0.00\\nATOM    517  N   ALA A  95      17.366   2.100 -12.534  1.00  0.00\\nATOM    518  CA  ALA A  95      17.441   3.251 -11.643  1.00  0.00\\nATOM    519  C   ALA A  95      18.521   3.060 -10.586  1.00  0.00\\nATOM    520  O   ALA A  95      19.312   3.967 -10.296  1.00  0.00\\nATOM    521  CB  ALA A  95       0.000   0.000   0.000  1.00  0.00\\nATOM    522  N   ALA A  96      18.524   1.872 -10.033  1.00  0.00\\nATOM    523  CA  ALA A  96      19.513   1.579  -9.003  1.00  0.00\\nATOM    524  C   ALA A  96      20.926   1.612  -9.571  1.00  0.00\\nATOM    525  O   ALA A  96      21.851   2.104  -8.912  1.00  0.00\\nATOM    526  CB  ALA A  96       0.000   0.000   0.000  1.00  0.00\\nATOM    527  N   ALA A  97      21.094   1.096 -10.781  1.00  0.00\\nATOM    528  CA  ALA A  97      22.413   1.086 -11.402  1.00  0.00\\nATOM    529  C   ALA A  97      22.937   2.502 -11.604  1.00  0.00\\nATOM    530  O   ALA A  97      24.134   2.757 -11.421  1.00  0.00\\nATOM    531  CB  ALA A  97       0.000   0.000   0.000  1.00  0.00\\nATOM    532  N   ALA A  98      22.084   3.379 -11.963  1.00  0.00\\nATOM    533  CA  ALA A  98      22.521   4.750 -12.201  1.00  0.00\\nATOM    534  C   ALA A  98      22.876   5.449 -10.895  1.00  0.00\\nATOM    535  O   ALA A  98      23.679   6.391 -10.888  1.00  0.00\\nATOM    536  CB  ALA A  98       0.000   0.000   0.000  1.00  0.00\\nATOM    537  N   ALA A  99      22.266   4.982  -9.768  1.00  0.00\\nATOM    538  CA  ALA A  99      22.590   5.604  -8.490  1.00  0.00\\nATOM    539  C   ALA A  99      23.656   4.810  -7.745  1.00  0.00\\nATOM    540  O   ALA A  99      23.991   5.138  -6.600  1.00  0.00\\nATOM    541  CB  ALA A  99       0.000   0.000   0.000  1.00  0.00\\nATOM    542  N   SER A 100      24.136   3.869  -8.328  1.00  0.00\\nATOM    543  CA  SER A 100      25.226   3.036  -7.834  1.00  0.00\\nATOM    544  C   SER A 100      24.695   1.838  -7.056  1.00  0.00\\nATOM    545  O   SER A 100      23.828   1.962  -6.229  1.00  0.00\\nATOM    546  CB  SER A 100       0.000   0.000   0.000  1.00  0.00\\nATOM    547  OG  SER A 100       0.000   0.000   0.000  1.00  0.00\\nHETATM  548 C21  OQO B 347       1.796   1.591   1.888  1.00  0.00           C\\nHETATM  549 C7   OQO B 347      -3.670  -3.928  -1.832  1.00  0.00           C\\nHETATM  550 C32  OQO B 347       4.744   4.449  -0.074  1.00  0.00           C\\nHETATM  551 C31  OQO B 347       6.015   3.877   0.007  1.00  0.00           C\\nHETATM  552 C20  OQO B 347       0.756   0.690   2.129  1.00  0.00           C\\nHETATM  553 C6   OQO B 347      -4.261  -4.765  -2.769  1.00  0.00           C\\nHETATM  554 C10  OQO B 347      -3.584  -0.488  -0.075  1.00  0.00           C\\nHETATM  555 C13  OQO B 347      -2.147  -2.160  -0.234  1.00  0.00           C\\nHETATM  556 C23  OQO B 347       2.321   0.302  -0.048  1.00  0.00           C\\nHETATM  557 C35  OQO B 347       1.998   5.388   0.829  1.00  0.00           C\\nHETATM  558 C22  OQO B 347       2.596   1.376   0.773  1.00  0.00           C\\nHETATM  559 C8   OQO B 347      -3.992  -2.556  -1.764  1.00  0.00           C\\nHETATM  560 C9   OQO B 347      -3.323  -1.716  -0.756  1.00  0.00           C\\nHETATM  561 C26  OQO B 347       3.754   2.272   0.494  1.00  0.00           C\\nHETATM  562 C33  OQO B 347       3.638   3.639   0.150  1.00  0.00           C\\nHETATM  563 C27  OQO B 347       5.041   1.731   0.564  1.00  0.00           C\\nHETATM  564 C29  OQO B 347       6.165   2.513   0.360  1.00  0.00           C\\nHETATM  565 C2   OQO B 347      -4.928  -2.088  -2.660  1.00  0.00           C\\nHETATM  566 C19  OQO B 347       0.532  -0.382   1.291  1.00  0.00           C\\nHETATM  567 C4   OQO B 347      -5.215  -4.204  -3.626  1.00  0.00           C\\nHETATM  568 C17  OQO B 347      -1.767  -4.259   2.637  1.00  0.00           C\\nHETATM  569 C18  OQO B 347      -2.012  -3.855   4.077  1.00  0.00           C\\nHETATM  570 C16  OQO B 347      -2.079  -2.810   2.972  1.00  0.00           C\\nHETATM  571 C1   OQO B 347      -5.349  -0.634  -2.677  1.00  0.00           C\\nHETATM  572 C15  OQO B 347      -0.976  -1.768   2.899  1.00  0.00           C\\nHETATM  573 C14  OQO B 347      -0.535  -1.455   1.452  1.00  0.00           C\\nHETATM  574 N11  OQO B 347      -2.585  -0.171   0.816  1.00  0.00           N\\nHETATM  575 N36  OQO B 347       0.754   5.663   0.496  1.00  0.00           N\\nHETATM  576 N3   OQO B 347      -5.530  -2.885  -3.584  1.00  0.00           N\\nHETATM  577 N37  OQO B 347       0.393   4.687  -0.396  1.00  0.00           N\\nHETATM  578 N38  OQO B 347       1.387   3.830  -0.620  1.00  0.00           N\\nHETATM  579 N12  OQO B 347      -1.758  -1.237   0.675  1.00  0.00           N\\nHETATM  580 N34  OQO B 347       2.394   4.279   0.159  1.00  0.00           N\\nHETATM  581 N24  OQO B 347       1.297  -0.544   0.210  1.00  0.00           N\\nHETATM  582 N5   OQO B 347      -5.850  -5.028  -4.591  1.00  0.00           N\\nHETATM  583 O25  OQO B 347       1.138  -1.534  -0.591  1.00  0.00           O\\nHETATM  584 F28  OQO B 347       5.155   0.395   0.915  1.00  0.00           F\\nHETATM  585 CL30 OQO B 347       7.700   1.769   0.497  1.00  0.00          CL\\nCONECT  548  552\\nCONECT  548  558\\nCONECT  549  553\\nCONECT  549  559\\nCONECT  550  551\\nCONECT  550  562\\nCONECT  551  550\\nCONECT  551  564\\nCONECT  552  548\\nCONECT  552  566\\nCONECT  553  549\\nCONECT  553  567\\nCONECT  554  560\\nCONECT  554  574\\nCONECT  555  560\\nCONECT  555  579\\nCONECT  556  558\\nCONECT  556  581\\nCONECT  557  575\\nCONECT  557  580\\nCONECT  558  548\\nCONECT  558  556\\nCONECT  558  561\\nCONECT  559  549\\nCONECT  559  560\\nCONECT  559  565\\nCONECT  560  554\\nCONECT  560  555\\nCONECT  560  559\\nCONECT  561  558\\nCONECT  561  562\\nCONECT  561  563\\nCONECT  562  550\\nCONECT  562  561\\nCONECT  562  580\\nCONECT  563  561\\nCONECT  563  564\\nCONECT  563  584\\nCONECT  564  551\\nCONECT  564  563\\nCONECT  564  585\\nCONECT  565  559\\nCONECT  565  571\\nCONECT  565  576\\nCONECT  566  552\\nCONECT  566  573\\nCONECT  566  581\\nCONECT  567  553\\nCONECT  567  576\\nCONECT  567  582\\nCONECT  568  569\\nCONECT  568  570\\nCONECT  569  568\\nCONECT  569  570\\nCONECT  570  568\\nCONECT  570  569\\nCONECT  570  572\\nCONECT  571  565\\nCONECT  572  570\\nCONECT  572  573\\nCONECT  573  566\\nCONECT  573  572\\nCONECT  573  579\\nCONECT  574  554\\nCONECT  574  579\\nCONECT  575  557\\nCONECT  575  577\\nCONECT  576  565\\nCONECT  576  567\\nCONECT  577  575\\nCONECT  577  578\\nCONECT  578  577\\nCONECT  578  580\\nCONECT  579  555\\nCONECT  579  573\\nCONECT  579  574\\nCONECT  580  557\\nCONECT  580  562\\nCONECT  580  578\\nCONECT  581  556\\nCONECT  581  566\\nCONECT  581  583\\nCONECT  582  567\\nCONECT  583  581\\nCONECT  584  563\\nCONECT  585  564\\n\",\"pdb\");\n",
              "\tviewer_17121814945186489.setStyle({\"chain\": \"A\"},{\"cartoon\": {\"color\": \"#33ff33\"}});\n",
              "\tviewer_17121814945186489.setStyle({\"chain\": \"B\"},{\"cartoon\": {\"color\": \"#00ffff\"}});\n",
              "\tviewer_17121814945186489.setStyle({\"chain\": \"B\"},{\"stick\": {}});\n",
              "\tviewer_17121814945186489.setStyle({\"chain\": \"C\"},{\"cartoon\": {\"color\": \"#ff33cc\"}});\n",
              "\tviewer_17121814945186489.setStyle({\"chain\": \"D\"},{\"cartoon\": {\"color\": \"#ffff00\"}});\n",
              "\tviewer_17121814945186489.setStyle({\"chain\": \"E\"},{\"cartoon\": {\"color\": \"#ff9999\"}});\n",
              "\tviewer_17121814945186489.setStyle({\"chain\": \"F\"},{\"cartoon\": {\"color\": \"#e5e5e5\"}});\n",
              "\tviewer_17121814945186489.setStyle({\"chain\": \"G\"},{\"cartoon\": {\"color\": \"#7f7fff\"}});\n",
              "\tviewer_17121814945186489.zoomTo();\n",
              "viewer_17121814945186489.render();\n",
              "});\n",
              "</script>"
            ]
          },
          "metadata": {},
          "output_type": "display_data"
        }
      ],
      "source": [
        "#@title Display 3D structure {run: \"auto\"}\n",
        "animate = \"interactive\" #@param [\"none\", \"movie\", \"interactive\"]\n",
        "color = \"chain\" #@param [\"rainbow\", \"chain\", \"plddt\"]\n",
        "denoise = True\n",
        "dpi = 100 #@param [\"100\", \"200\", \"400\"] {type:\"raw\"}\n",
        "\n",
        "from colabdesign.shared.plot import pymol_color_list\n",
        "from colabdesign.rf.utils import get_ca, get_Ls, make_animation\n",
        "from string import ascii_uppercase, ascii_lowercase\n",
        "import os\n",
        "import ipywidgets as widgets\n",
        "from IPython.display import display, HTML\n",
        "import py3Dmol\n",
        "\n",
        "alphabet_list = list(ascii_uppercase + ascii_lowercase)\n",
        "\n",
        "\n",
        "# Construct the base output directory\n",
        "base_output_dir = os.path.join(OUTPUT_DIR, output_subfolder)\n",
        "\n",
        "def find_latest_output_dir(base_dir, prefix):\n",
        "    \"\"\"Find the latest output directory based on the prefix.\"\"\"\n",
        "    dirs = [d for d in os.listdir(base_dir) if os.path.isdir(os.path.join(base_dir, d)) and d.startswith(prefix)]\n",
        "    if not dirs:\n",
        "        raise FileNotFoundError(f\"No output directories found with prefix '{prefix}' in '{base_dir}'\")\n",
        "    latest_dir = sorted(dirs, key=lambda x: int(x.split('_')[-1]))[-1]\n",
        "    return os.path.join(base_dir, latest_dir)\n",
        "\n",
        "def plot_pdb(num=0):\n",
        "    # Find the latest output directory\n",
        "    latest_output_dir = find_latest_output_dir(base_output_dir, output_prefix)\n",
        "\n",
        "    # Construct the path to the PDB file\n",
        "    pdb_path = os.path.join(latest_output_dir, f\"{output_prefix}_{num}.pdb\")\n",
        "\n",
        "    # Load the PDB file\n",
        "    pdb_str = open(pdb_path, 'r').read()\n",
        "\n",
        "    # Initialize the 3Dmol.js viewer\n",
        "    view = py3Dmol.view(js='https://3dmol.org/build/3Dmol.js')\n",
        "    view.addModel(pdb_str, 'pdb')\n",
        "\n",
        "    # Apply color scheme\n",
        "    if color == \"rainbow\":\n",
        "        view.setStyle({'cartoon': {'color':'spectrum'}})\n",
        "    elif color == \"chain\":\n",
        "        # Example: Apply color by chain\n",
        "        for n, chain, c in zip(range(len(contigs)), alphabet_list, pymol_color_list):\n",
        "            view.setStyle({'chain': chain}, {'cartoon': {'color': c}})\n",
        "            # If chain == B the visualization should be atoms\n",
        "            if chain == \"B\":\n",
        "                view.setStyle({'chain': chain}, {'stick': {}})\n",
        "    else:\n",
        "        # Example: Apply a custom color scheme\n",
        "        view.setStyle({'cartoon': {'colorscheme': {'prop':'b','gradient': 'roygb','min':0.5,'max':0.9}}})\n",
        "\n",
        "    # Zoom to fit and display the viewer\n",
        "    view.zoomTo()\n",
        "    view.show()\n",
        "\n",
        "\n",
        "\n",
        "if num_designs > 1:\n",
        "  output = widgets.Output()\n",
        "  def on_change(change):\n",
        "    if change['name'] == 'value':\n",
        "      with output:\n",
        "        output.clear_output(wait=True)\n",
        "        plot_pdb(change['new'])\n",
        "  dropdown = widgets.Dropdown(\n",
        "      options=[(f'{k}',k) for k in range(num_designs)],\n",
        "      value=0, description='design:',\n",
        "  )\n",
        "  dropdown.observe(on_change)\n",
        "  display(widgets.VBox([dropdown, output]))\n",
        "  with output:\n",
        "    plot_pdb(dropdown.value)\n",
        "else:\n",
        "  plot_pdb()"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "cellView": "form",
        "id": "PhJ2xFUqRSt1"
      },
      "outputs": [],
      "source": [
        "#@title Package and download results\n",
        "#@markdown If you are having issues downloading the result archive,\n",
        "#@markdown try disabling your adblocker and run this cell again.\n",
        "#@markdown  If that fails click on the little folder icon to the\n",
        "#@markdown  left, navigate to file: `name.result.zip`,\n",
        "#@markdown  right-click and select \\\"Download\\\"\n",
        "#@markdown (see [screenshot](https://pbs.twimg.com/media/E6wRW2lWUAEOuoe?format=jpg&name=small)).\n",
        "import shutil\n",
        "\n",
        "def zip_last_job(final_output_path, counter):\n",
        "    \"\"\"\n",
        "    Zip the last job's output directory for download.\n",
        "    \"\"\"\n",
        "    base_output_path = os.path.join(OUTPUT_DIR, final_output_path)\n",
        "\n",
        "    if final_output_path:\n",
        "        output_path = f\"{base_output_path}\"\n",
        "        shutil.make_archive(output_path, 'zip', output_path)\n",
        "        return f\"{output_path}.zip\"\n",
        "    else:\n",
        "        print(\"No output directory found.\")\n",
        "        return None\n",
        "\n",
        "\n",
        "# Assuming you're in a Jupyter notebook cell\n",
        "from google.colab import files\n",
        "\n",
        "# This cell should be run after the diffusion function to zip and download the output\n",
        "zip_path = zip_last_job(final_output_path=final_output_path, counter=0)\n",
        "\n",
        "if zip_path and is_colab():\n",
        "    from google.colab import files\n",
        "    files.download(zip_path)\n",
        "else:\n",
        "    print(\"Zip file path:\", zip_path)\n",
        "    print(\"Note: Automatic download is only supported in Google Colab.\")"
      ]
    }
  ],
  "metadata": {
    "accelerator": "GPU",
    "colab": {
      "gpuType": "V100",
      "private_outputs": true,
      "provenance": []
    },
    "kernelspec": {
      "display_name": "Python 3",
      "name": "python3"
    },
    "language_info": {
      "codemirror_mode": {
        "name": "ipython",
        "version": 3
      },
      "file_extension": ".py",
      "mimetype": "text/x-python",
      "name": "python",
      "nbconvert_exporter": "python",
      "pygments_lexer": "ipython3",
      "version": "3.10.12"
    }
  },
  "nbformat": 4,
  "nbformat_minor": 0
}