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ChrisWellsWood/Anti-parallel Optimisation.ipynb

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A quick overview of how to use a custom specification with an optimizer in ISAMBARD.
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Anti-parallel Optimisation.ipynb
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Using Custom Specifications with the Optmizers"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"In this example, we're going to make a custom `specification` that can create anti-parallel, homodimeric coiled coils. We need to write a small wrapper around our existing `CoiledCoil` class to do this, but it's not too much work."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"First, we'll import all the modules we'll need:"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import budeff\n",
"import isambard\n",
"import isambard.modelling as modelling\n",
"import isambard.optimisation as optimisation\n",
"import isambard.specifications as specifications\n",
"import matplotlib.pyplot as plt\n",
"\n",
"# This is to make matplotlib plot with svg\n",
"%config InlineBackend.figure_format = 'svg'"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now we can create our custom specification. We use a property of Python classes called \"inheritence\". This is quite an advanced feature, but it's simple to understand. We want to create a new class that builds on top of the functionality of an existing class, in this case `CoiledCoil`. `CoiledCoil` has all the functionality we need, but we want it to take a different set of parameters as the input.\n",
"\n",
"Let's take a look at all the functionality that coiled coil has, then we can figure out how we're going to change it. To see all the attributes and methods, you could look at the source code, or we can pull out the help string:"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Help on class CoiledCoil in module isambard.specifications.coiledcoil:\n",
"\n",
"class CoiledCoil(ampal.assembly.Assembly)\n",
" | CoiledCoil(n, auto_build=True)\n",
" | \n",
" | Models a coiled-coil protein.\n",
" | \n",
" | Notes\n",
" | -----\n",
" | Instantiating this class using just an oligomeric state is used\n",
" | to create simple reference models. To build more complex models\n",
" | use the `from_parameters` classmethod.\n",
" | \n",
" | Parameters\n",
" | ----------\n",
" | n : int\n",
" | The oligomeric state of the model to be built.\n",
" | auto_build : bool, optional\n",
" | If `True`, the model will be built as part of instantiation.\n",
" | \n",
" | Attributes\n",
" | ----------\n",
" | aas : [int]\n",
" | Number of amino acids in each minor helix.\n",
" | basis_set_sequences : [str]\n",
" | Reference sequences for the oligomeric state that has been\n",
" | selected, taken from the basis set of coiled coils.\n",
" | major_radii : [float]\n",
" | Radii of the minor helices relative to the super-helical\n",
" | axis.\n",
" | major_pitches : [float]\n",
" | Pitch values of the minor helices relative to the super-helical\n",
" | axis.\n",
" | phi_c_alphas :\n",
" | Relative rotation values of the minor helices relative to\n",
" | the super-helical axis.\n",
" | minor_helix_types : [str]\n",
" | Helix types of the minor helices. Can be: 'alpha', 'pi', '3-10',\n",
" | 'PPI', 'PP2', 'collagen'.\n",
" | major_handedness : str\n",
" | Handedness of the super helix.\n",
" | orientations :\n",
" | Orientation of helices relative to the super-helical axis. 1\n",
" | is parallel, -1 is anti-parallel.\n",
" | minor_repeats : [float]\n",
" | Hydrophobic repeats of the minor helices.\n",
" | rotational_offsets :\n",
" | Rotation of the minor helices relative to the super-helical\n",
" | axis.\n",
" | z_shifts : [float]\n",
" | Translation of the minor helices along the super-helical axis.\n",
" | oligomeric_state : int\n",
" | Oligomeric state of the coiled coil.\n",
" | \n",
" | Method resolution order:\n",
" | CoiledCoil\n",
" | ampal.assembly.Assembly\n",
" | ampal.base_ampal.BaseAmpal\n",
" | builtins.object\n",
" | \n",
" | Methods defined here:\n",
" | \n",
" | __init__(self, n, auto_build=True)\n",
" | Initialize self. See help(type(self)) for accurate signature.\n",
" | \n",
" | build(self)\n",
" | Builds a model of a coiled coil protein using input parameters.\n",
" | \n",
" | ----------------------------------------------------------------------\n",
" | Class methods defined here:\n",
" | \n",
" | from_parameters(n, aa=28, major_radius=None, major_pitch=None, phi_c_alpha=26.42, minor_helix_type='alpha', auto_build=True) from builtins.type\n",
" | Creates a `CoiledCoil` from defined super-helical parameters.\n",
" | \n",
" | Parameters\n",
" | ----------\n",
" | n : int\n",
" | Oligomeric state\n",
" | aa : int, optional\n",
" | Number of amino acids per minor helix.\n",
" | major_radius : float, optional\n",
" | Radius of super helix.\n",
" | major_pitch : float, optional\n",
" | Pitch of super helix.\n",
" | phi_c_alpha : float, optional\n",
" | Rotation of minor helices relative to the super-helical\n",
" | axis.\n",
" | minor_helix_type : float, optional\n",
" | Helix type of minor helices. Can be: 'alpha', 'pi', '3-10',\n",
" | 'PPI', 'PP2', 'collagen'.\n",
" | auto_build : bool, optional\n",
" | If `True`, the model will be built as part of instantiation.\n",
" | \n",
" | from_polymers(polymers) from builtins.type\n",
" | Creates a `CoiledCoil` from a list of `HelicalHelices`.\n",
" | \n",
" | Parameters\n",
" | ----------\n",
" | polymers : [HelicalHelix]\n",
" | List of `HelicalHelices`.\n",
" | \n",
" | tropocollagen(aa=28, major_radius=5.0, major_pitch=85.0, auto_build=True) from builtins.type\n",
" | Creates a model of a collagen triple helix.\n",
" | \n",
" | Parameters\n",
" | ----------\n",
" | aa : int, optional\n",
" | Number of amino acids per minor helix.\n",
" | major_radius : float, optional\n",
" | Radius of super helix.\n",
" | major_pitch : float, optional\n",
" | Pitch of super helix.\n",
" | auto_build : bool, optional\n",
" | If `True`, the model will be built as part of instantiation.\n",
" | \n",
" | ----------------------------------------------------------------------\n",
" | Methods inherited from ampal.assembly.Assembly:\n",
" | \n",
" | __add__(self, other)\n",
" | Merges together two `Assemblies`.\n",
" | \n",
" | Raises\n",
" | ------\n",
" | TypeError\n",
" | Raised if other is any type other than `Assembly`.\n",
" | \n",
" | __getitem__(self, item)\n",
" | \n",
" | __len__(self)\n",
" | \n",
" | __repr__(self)\n",
" | Return repr(self).\n",
" | \n",
" | append(self, item)\n",
" | Adds a `Polymer` to the `Assembly`.\n",
" | \n",
" | Raises\n",
" | ------\n",
" | TypeError\n",
" | Raised if other is any type other than `Polymer`.\n",
" | \n",
" | extend(self, assembly)\n",
" | Extends the `Assembly` with the contents of another `Assembly`.\n",
" | \n",
" | Raises\n",
" | ------\n",
" | TypeError\n",
" | Raised if other is any type other than `Assembly`.\n",
" | \n",
" | filter_mol_types(self, mol_types)\n",
" | \n",
" | get_atoms(self, ligands=True, pseudo_group=False, inc_alt_states=False)\n",
" | Flat list of all the `Atoms` in the `Assembly`.\n",
" | \n",
" | Parameters\n",
" | ----------\n",
" | ligands : bool, optional\n",
" | Include ligand `Atoms`.\n",
" | pseudo_group : bool, optional\n",
" | Include pseudo_group `Atoms`.\n",
" | inc_alt_states : bool, optional\n",
" | Include alternate sidechain conformations.\n",
" | \n",
" | Returns\n",
" | -------\n",
" | atoms : itertools.chain\n",
" | All the `Atoms` as a iterator.\n",
" | \n",
" | get_ligands(self, solvent=True)\n",
" | Retrieves all ligands from the `Assembly`.\n",
" | \n",
" | Parameters\n",
" | ----------\n",
" | solvent : bool, optional\n",
" | If `True`, solvent molecules will be included.\n",
" | \n",
" | get_monomers(self, ligands=True, pseudo_group=False)\n",
" | Retrieves all the `Monomers` from the `Assembly` object.\n",
" | \n",
" | Parameters\n",
" | ----------\n",
" | ligands : bool, optional\n",
" | If `true`, will include ligand `Monomers`.\n",
" | pseudo_group : bool, optional\n",
" | If `True`, will include pseudo atoms.\n",
" | \n",
" | is_within(self, cutoff_dist, point, ligands=True)\n",
" | Returns all atoms in AMPAL object within `cut-off` distance from the `point`.\n",
" | \n",
" | make_pdb(self, ligands=True, alt_states=False, pseudo_group=False, header=True, footer=True)\n",
" | Generates a PDB string for the Assembly.\n",
" | \n",
" | Parameters\n",
" | ----------\n",
" | ligands : bool, optional\n",
" | If `True`, will include ligands in the output.\n",
" | alt_states : bool, optional\n",
" | If `True`, will include alternate conformations in the output.\n",
" | pseudo_group : bool, optional\n",
" | If `True`, will include pseudo atoms in the output.\n",
" | header : bool, optional\n",
" | If `True` will write a header for output.\n",
" | footer : bool, optional\n",
" | If `True` will write a footer for output.\n",
" | \n",
" | Returns\n",
" | -------\n",
" | pdb_str : str\n",
" | String of the pdb for the Assembly. Generated by collating\n",
" | Polymer().pdb calls for the component Polymers.\n",
" | \n",
" | relabel_all(self)\n",
" | Relabels all Polymers, Monomers and Atoms with default labeling.\n",
" | \n",
" | relabel_atoms(self, start=1)\n",
" | Relabels all Atoms in numerical order, offset by the start parameter.\n",
" | \n",
" | Parameters\n",
" | ----------\n",
" | start : int, optional\n",
" | Defines an offset for the labelling.\n",
" | \n",
" | relabel_monomers(self)\n",
" | Relabels all Monomers in the component Polymers in numerical order.\n",
" | \n",
" | relabel_polymers(self, labels=None)\n",
" | Relabels the component Polymers either in alphabetical order or\n",
" | using a list of labels.\n",
" | \n",
" | Parameters\n",
" | ----------\n",
" | labels : list, optional\n",
" | A list of new labels.\n",
" | \n",
" | Raises\n",
" | ------\n",
" | ValueError\n",
" | Raised if the number of labels does not match the number of\n",
" | component Polymer objects.\n",
" | \n",
" | tag_atoms_unique_ids(self, force=False)\n",
" | Tags each Atom in the Assembly with its unique_id.\n",
" | \n",
" | Notes\n",
" | -----\n",
" | The unique_id for each atom is a tuple (a double). `unique_id[0]`\n",
" | is the unique_id for its parent `Monomer` (see `Monomer.unique_id`\n",
" | for more information). `unique_id[1]` is the atom_type in the\n",
" | `Assembly` as a string, e.g. 'CA', 'CD2'.\n",
" | \n",
" | Parameters\n",
" | ----------\n",
" | force : bool, optional\n",
" | If True the tag will be run even if Atoms are already tagged.\n",
" | If False, only runs if at least one Atom is not tagged.\n",
" | \n",
" | tag_ca_geometry(self, force=False, reference_axis=None, reference_axis_name='ref_axis')\n",
" | Tags each `Monomer` in the `Assembly` with its helical geometry.\n",
" | \n",
" | Parameters\n",
" | ----------\n",
" | force : bool, optional\n",
" | If True the tag will be run even if `Monomers` are already tagged.\n",
" | reference_axis : list(numpy.array or tuple or list), optional\n",
" | Coordinates to feed to geometry functions that depend on\n",
" | having a reference axis.\n",
" | reference_axis_name : str, optional\n",
" | Used to name the keys in tags at `Chain` and `Residue` level.\n",
" | \n",
" | tag_torsion_angles(self, force=False)\n",
" | Tags each `Monomer` in the `Assembly` with its torsion angles.\n",
" | \n",
" | Parameters\n",
" | ----------\n",
" | force : bool, optional\n",
" | If `True`, the tag will be run even if `Monomers` are already\n",
" | tagged.\n",
" | \n",
" | ----------------------------------------------------------------------\n",
" | Data descriptors inherited from ampal.assembly.Assembly:\n",
" | \n",
" | backbone\n",
" | Generates a new `Assembly` containing only the backbone atoms.\n",
" | \n",
" | Notes\n",
" | -----\n",
" | Metadata is not currently preserved from the parent object.\n",
" | Sequence data is retained, but only the main chain atoms are\n",
" | retained.\n",
" | \n",
" | Returns\n",
" | -------\n",
" | bb_assembly : ampal.Protein\n",
" | `Assembly` containing only the backbone atoms of the original\n",
" | `Assembly`.\n",
" | \n",
" | fasta\n",
" | Generates a FASTA string for the `Assembly`.\n",
" | \n",
" | Notes\n",
" | -----\n",
" | Explanation of FASTA format: https://en.wikipedia.org/wiki/FASTA_format\n",
" | Recommendation that all lines of text be shorter than 80\n",
" | characters is adhered to. Format of PDBID|CHAIN|SEQUENCE is \n",
" | consistent with files downloaded from the PDB. Uppercase \n",
" | PDBID used for consistency with files downloaded from the PDB.\n",
" | Useful for feeding into cdhit and then running sequence clustering.\n",
" | \n",
" | Returns\n",
" | -------\n",
" | fasta_str : str\n",
" | String of the fasta file for the `Assembly`.\n",
" | \n",
" | isoelectric_point\n",
" | Returns the isoelectric point of the `Assembly`.\n",
" | \n",
" | molar_extinction_280\n",
" | Returns the extinction co-efficient of the `Assembly` at 280 nm.\n",
" | \n",
" | molecular_weight\n",
" | Returns the molecular weight of the `Assembly` in Daltons.\n",
" | \n",
" | pdb\n",
" | Runs make_pdb in default mode.\n",
" | \n",
" | primitives\n",
" | Generates a new `Assembly` containing the primitives of each Polymer.\n",
" | \n",
" | Notes\n",
" | -----\n",
" | Metadata is not currently preserved from the parent object.\n",
" | \n",
" | Returns\n",
" | -------\n",
" | prim_assembly : ampal.Protein\n",
" | `Assembly` containing only the primitives of the `Polymers`\n",
" | in the original `Assembly`.\n",
" | \n",
" | sequences\n",
" | Returns the sequence of each `Polymer` in the `Assembly` as a list.\n",
" | \n",
" | Returns\n",
" | -------\n",
" | sequences : [str]\n",
" | List of sequences.\n",
" | \n",
" | ----------------------------------------------------------------------\n",
" | Methods inherited from ampal.base_ampal.BaseAmpal:\n",
" | \n",
" | rmsd(self, other, backbone=False)\n",
" | Calculates the RMSD between two AMPAL objects.\n",
" | \n",
" | Notes\n",
" | -----\n",
" | No fitting operation is performs and both AMPAL objects must\n",
" | have the same number of atoms.\n",
" | \n",
" | Parameters\n",
" | ----------\n",
" | other : AMPAL Object\n",
" | Any AMPAL object with `get_atoms` method.\n",
" | backbone : bool, optional\n",
" | Calculates RMSD of backbone only.\n",
" | \n",
" | rotate(self, angle, axis, point=None, radians=False, inc_alt_states=True)\n",
" | Rotates every atom in the AMPAL object.\n",
" | \n",
" | Parameters\n",
" | ----------\n",
" | angle : float\n",
" | Angle that AMPAL object will be rotated.\n",
" | axis : 3D Vector (tuple, list, numpy.array)\n",
" | Axis about which the AMPAL object will be rotated.\n",
" | point : 3D Vector (tuple, list, numpy.array), optional\n",
" | Point that the axis lies upon. If `None` then the origin is used.\n",
" | radians : bool, optional\n",
" | True is `angle` is define in radians, False is degrees.\n",
" | inc_alt_states : bool, optional\n",
" | If true, will rotate atoms in all states i.e. includes\n",
" | alternate conformations for sidechains.\n",
" | \n",
" | translate(self, vector, inc_alt_states=True)\n",
" | Translates every atom in the AMPAL object.\n",
" | \n",
" | Parameters\n",
" | ----------\n",
" | vector : 3D Vector (tuple, list, numpy.array)\n",
" | Vector used for translation.\n",
" | inc_alt_states : bool, optional\n",
" | If true, will rotate atoms in all states i.e. includes\n",
" | alternate conformations for sidechains.\n",
" | \n",
" | ----------------------------------------------------------------------\n",
" | Data descriptors inherited from ampal.base_ampal.BaseAmpal:\n",
" | \n",
" | __dict__\n",
" | dictionary for instance variables (if defined)\n",
" | \n",
" | __weakref__\n",
" | list of weak references to the object (if defined)\n",
" | \n",
" | centre_of_mass\n",
" | Returns the centre of mass of AMPAL object.\n",
" | \n",
" | Notes\n",
" | -----\n",
" | All atoms are included in calculation, call `centre_of_mass`\n",
" | manually if another selection is require.\n",
" | \n",
" | Returns\n",
" | -------\n",
" | centre_of_mass : numpy.array\n",
" | 3D coordinate for the centre of mass.\n",
"\n"
]
}
],
"source": [
"help(specifications.CoiledCoil)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"We need more granular control of the parameters than when making a parallel-coiled coil, so we won't use `CoiledCoil.from_parameters` to make the class, instead we'll call `CoiledCoil` directly then redefine the relevant default parameter values. As we're making an anti-parallel, homodimeric coiled coil, we can define its structure with 5 parameters: the length of each helix, the radius of the bundle, the pitch of the superhelix, the relative rotate of the component helices (phi Ca) and the translation of one helix relative to the other helix along the superhelical axis (z-shift). That means we'll need to redefine the attributes `aas`, `major_radii`, `major_pitch`, `z_shifts` and `phi_c_alphas`, you should see these in the parameters section of the help string printed above.\n",
"\n",
"> Note: If we wanted to make heterodimeric coiled coils, we'd need to give 2 phi Ca parameters, but as we're making a homodimer, we only need one.\n",
"\n",
"Let's make our custom specification:"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"class APHomoDimer(specifications.CoiledCoil):\n",
" \"\"\"Specification for creating anti-parallel, homodimeric coiled coils.\"\"\"\n",
" \n",
" # As this specification is only for making dimers, the oligomeric state is fixed\n",
" # for all instances of this class, so it's good practice to define that here.\n",
" # Variables defined like this are called `class attributes` and are shared between\n",
" # all instances of the class\n",
" oligomeric_state = 2\n",
" \n",
" # The only thing that we need to define is a new `__init__` method, which defines\n",
" # how the class is created. We get all the rest of the functionality off the\n",
" # parent class `CoiledCoil`.\n",
" def __init__(self, helix_length, radius, pitch, phica, zshift):\n",
" # To kick everything off, this class runs the standard setup of the `CoiledCoil`\n",
" # class, which gives our class all of the same attributes and methods. The\n",
" # `super` function gives us access to the parent class. As we want to modify\n",
" # some of the parameters before building the model, we set `auto_build` to false\n",
" super().__init__(self.oligomeric_state, auto_build=False)\n",
" \n",
" # Next, we redefine the relevant default values that `CoiledCoil` has set. As\n",
" # we have 2 helices, we have 2 values for each of these, but in this case they\n",
" # are the same as we're making a homodimer\n",
" self.aas = [helix_length, helix_length]\n",
" self.major_radii = [radius, radius]\n",
" self.major_pitches = [pitch, pitch]\n",
" self.z_shifts = [0, zshift]\n",
" self.phi_c_alphas = [phica, phica]\n",
" \n",
" # We need to set the orientation of the helices to be anti-parallel, so one\n",
" # needs to have a +1 orientation and the other needs a -1 orientation\n",
" self.orientations = [1, -1]\n",
" \n",
" # Now we've redefined these values, we need to build the model from these\n",
" # parameters. We can do this using the build method, which comes from\n",
" # `CoiledCoil`\n",
" self.build()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Let's make sure that works as expected:"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"test_ap_dimer = APHomoDimer(helix_length=28, radius=5.0, pitch=200, phica=283, zshift=10)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<Assembly containing 2 Polypeptides>\n"
]
}
],
"source": [
"print(test_ap_dimer)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['GGGGGGGGGGGGGGGGGGGGGGGGGGGG', 'GGGGGGGGGGGGGGGGGGGGGGGGGGGG']"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"test_ap_dimer.sequences"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"That looks good, it's just the backbone (hence the poly G sequence) but it looks like it's made a model. You could write this to a pdb file and check it if you like.\n",
"\n",
"Everything from here is pretty much the same as a standard optimisation, you need to:\n",
"\n",
"1. Define a scoring function\n",
"1. Define sequences\n",
"1. Define a list of parameters to be optimised\n",
"1. Create the optimizer\n",
"1. Run the optimisation\n",
"\n",
"Let's do that:"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"def get_buff_total_energy(ampal_object):\n",
" return budeff.get_internal_energy(ampal_object).total_energy"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
"sequences = ['EIAALKQEIAALKKENAALKWEIAALKQ', 'EIAALKQEIAALKKENAALKWEIAALKQ']"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"parameters = [\n",
" optimisation.Parameter.static('Helix Length', 28),\n",
" optimisation.Parameter.dynamic('Radius', 5.0, 1.0),\n",
" optimisation.Parameter.dynamic('Pitch', 200, 60),\n",
" optimisation.Parameter.dynamic('PhiCA', 283, 27),\n",
" optimisation.Parameter.dynamic('ZShift', 10, 10),\n",
"]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The parameters defined above match the `__init__` signature of the `APHomoDimer` class. We're fixing helix length and varying the radius, pitch, phi CA and z-shift."
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"gen\tevals\tavg \tstd \tmin \tmax \n",
"0 \t67 \t-717.035\t56.3382\t-779.039\t-575.02\n",
"1 \t71 \t-759.92 \t9.8138 \t-793.417\t-735.209\n",
"2 \t84 \t-768.834\t7.85986\t-795.953\t-759.069\n",
"3 \t64 \t-774.292\t8.486 \t-795.953\t-764.014\n",
"4 \t76 \t-783.952\t8.36001\t-795.953\t-771.728\n",
"Evaluated 462 models in total in 0:00:28.725088\n",
"Best fitness is (-795.9534961676324,)\n",
"Best parameters are [28, 5.048127474280228, 156.87381055854397, 256.4891626134463, 10.61497485215419]\n",
"Warning! Parameter 3 is at or near minimum allowed value\n",
"\n"
]
}
],
"source": [
"optimizer = optimisation.GA(APHomoDimer, sequences, parameters, get_buff_total_energy)\n",
"optimizer.run_opt(100, 5, cores=4)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"We can perform all the same analysis after the optimisation, our new specification looks like any other specification to ISAMBARD."
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
"funnel_data = optimizer.make_energy_funnel_data(cores=4)"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [],
"source": [
"xs = [x[0] for x in funnel_data]\n",
"ys = [x[1] for x in funnel_data]\n",
"zs = [x[2] for x in funnel_data]"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
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"text/plain": [
"<Figure size 288x288 with 1 Axes>"
]
},
"metadata": {
"needs_background": "light"
},
"output_type": "display_data"
}
],
"source": [
"fig, ax = plt.subplots(1, 1)\n",
"fig.set_size_inches(4, 4)\n",
"ax.grid()\n",
"ax.scatter(xs, ys, c=zs)\n",
"ax.set_xlabel('RMSD (Å)')\n",
"ax.set_ylabel('BUFF Internal Energy')\n",
"None"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
"with open(\"best_ap_dimer.pdb\", \"w\") as outf:\n",
" outf.write(optimizer.best_model.pdb)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Conclusions"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"If you want to make a varient of an existing specification in ISAMBARD, you can use Python inheritence to get a lot of functionality for free. Going beyond this, you could make completely new specification, all you need to do is make sure your new specification inherits from `ampal.Assembly`, take a look at the `CoiledCoil` source code as an example."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"> ### Problem\n",
"> Try making a new specification to create an antiparallel *hetero*dimer, it should have 2 phi Ca values."
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
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"name": "ipython",
"version": 3
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"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
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"nbformat": 4,
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Raw
best_ap_dimer.pdb
HEADER ISAMBARD Model
ATOM 1 N GLU A 1 -6.026 -1.296 9.965 1.00 0.00 N
ATOM 2 CA GLU A 1 -5.585 -2.191 11.061 1.00 0.00 C
ATOM 3 C GLU A 1 -4.628 -1.419 11.970 1.00 0.00 C
ATOM 4 O GLU A 1 -4.654 -1.565 13.194 1.00 0.00 O
ATOM 5 CB GLU A 1 -4.922 -3.447 10.493 1.00 0.00 C
ATOM 6 CD GLU A 1 -5.183 -5.593 9.185 1.00 0.00 C
ATOM 7 CG GLU A 1 -5.885 -4.399 9.802 1.00 0.00 C
ATOM 8 OE1 GLU A 1 -3.936 -5.584 9.130 1.00 0.00 O
ATOM 9 OE2 GLU A 1 -5.881 -6.536 8.757 1.00 0.00 O
ATOM 10 N ILE A 2 -3.769 -0.637 11.353 1.00 0.00 N
ATOM 11 CA ILE A 2 -2.745 0.136 12.097 1.00 0.00 C
ATOM 12 C ILE A 2 -3.453 1.171 12.972 1.00 0.00 C
ATOM 13 O ILE A 2 -3.046 1.432 14.106 1.00 0.00 O
ATOM 14 CB ILE A 2 -1.741 0.808 11.142 1.00 0.00 C
ATOM 15 CD1 ILE A 2 -0.071 0.300 9.285 1.00 0.00 C
ATOM 16 CG1 ILE A 2 -0.894 -0.248 10.429 1.00 0.00 C
ATOM 17 CG2 ILE A 2 -0.880 1.811 11.894 1.00 0.00 C
ATOM 18 N ALA A 3 -4.491 1.791 12.423 1.00 0.00 N
ATOM 19 CA ALA A 3 -5.233 2.847 13.152 1.00 0.00 C
ATOM 20 C ALA A 3 -5.912 2.218 14.370 1.00 0.00 C
ATOM 21 O ALA A 3 -5.973 2.816 15.446 1.00 0.00 O
ATOM 22 CB ALA A 3 -6.246 3.513 12.234 1.00 0.00 C
ATOM 23 N ALA A 4 -6.471 1.040 14.201 1.00 0.00 N
ATOM 24 CA ALA A 4 -7.187 0.333 15.290 1.00 0.00 C
ATOM 25 C ALA A 4 -6.184 -0.021 16.389 1.00 0.00 C
ATOM 26 O ALA A 4 -6.490 0.056 17.580 1.00 0.00 O
ATOM 27 CB ALA A 4 -7.880 -0.909 14.750 1.00 0.00 C
ATOM 28 N LEU A 5 -5.016 -0.449 15.982 1.00 0.00 N
ATOM 29 CA LEU A 5 -3.953 -0.870 16.926 1.00 0.00 C
ATOM 30 C LEU A 5 -3.504 0.347 17.735 1.00 0.00 C
ATOM 31 O LEU A 5 -3.231 0.251 18.933 1.00 0.00 O
ATOM 32 CB LEU A 5 -2.782 -1.498 16.168 1.00 0.00 C
ATOM 33 CG LEU A 5 -3.053 -2.846 15.497 1.00 0.00 C
ATOM 34 CD1 LEU A 5 -1.869 -3.268 14.640 1.00 0.00 C
ATOM 35 CD2 LEU A 5 -3.361 -3.912 16.536 1.00 0.00 C
ATOM 36 N LYS A 6 -3.397 1.478 17.054 1.00 0.00 N
ATOM 37 CA LYS A 6 -2.922 2.724 17.703 1.00 0.00 C
ATOM 38 C LYS A 6 -3.944 3.147 18.760 1.00 0.00 C
ATOM 39 O LYS A 6 -3.585 3.621 19.839 1.00 0.00 O
ATOM 40 CB LYS A 6 -2.710 3.824 16.661 1.00 0.00 C
ATOM 41 CD LYS A 6 -1.383 4.706 14.722 1.00 0.00 C
ATOM 42 CE LYS A 6 -0.199 4.467 13.799 1.00 0.00 C
ATOM 43 CG LYS A 6 -1.527 3.584 15.737 1.00 0.00 C
ATOM 44 NZ LYS A 6 -0.071 5.537 12.771 1.00 0.00 N
ATOM 45 N GLN A 7 -5.222 3.023 18.439 1.00 0.00 N
ATOM 46 CA GLN A 7 -6.306 3.431 19.364 1.00 0.00 C
ATOM 47 C GLN A 7 -6.261 2.532 20.600 1.00 0.00 C
ATOM 48 O GLN A 7 -6.479 2.984 21.726 1.00 0.00 O
ATOM 49 CB GLN A 7 -7.665 3.350 18.666 1.00 0.00 C
ATOM 50 CD GLN A 7 -9.188 4.230 16.852 1.00 0.00 C
ATOM 51 CG GLN A 7 -7.865 4.390 17.575 1.00 0.00 C
ATOM 52 OE1 GLN A 7 -9.748 3.135 16.799 1.00 0.00 O
ATOM 53 NE2 GLN A 7 -9.692 5.324 16.294 1.00 0.00 N
ATOM 54 N GLU A 8 -6.034 1.260 20.394 1.00 0.00 N
ATOM 55 CA GLU A 8 -5.994 0.263 21.490 1.00 0.00 C
ATOM 56 C GLU A 8 -4.806 0.581 22.399 1.00 0.00 C
ATOM 57 O GLU A 8 -4.889 0.457 23.623 1.00 0.00 O
ATOM 58 CB GLU A 8 -5.898 -1.154 20.922 1.00 0.00 C
ATOM 59 CD GLU A 8 -7.000 -3.006 19.605 1.00 0.00 C
ATOM 60 CG GLU A 8 -7.154 -1.623 20.206 1.00 0.00 C
ATOM 61 OE1 GLU A 8 -5.862 -3.519 19.579 1.00 0.00 O
ATOM 62 OE2 GLU A 8 -8.018 -3.576 19.159 1.00 0.00 O
ATOM 63 N ILE A 9 -3.703 0.947 21.781 1.00 0.00 N
ATOM 64 CA ILE A 9 -2.454 1.237 22.526 1.00 0.00 C
ATOM 65 C ILE A 9 -2.681 2.471 23.401 1.00 0.00 C
ATOM 66 O ILE A 9 -2.204 2.544 24.535 1.00 0.00 O
ATOM 67 CB ILE A 9 -1.263 1.443 21.572 1.00 0.00 C
ATOM 68 CD1 ILE A 9 0.353 0.113 23.027 1.00 0.00 C
ATOM 69 CG1 ILE A 9 0.053 1.433 22.353 1.00 0.00 C
ATOM 70 CG2 ILE A 9 -1.437 2.723 20.770 1.00 0.00 C
ATOM 71 N ALA A 10 -3.378 3.459 22.852 1.00 0.00 N
ATOM 72 CA ALA A 10 -3.628 4.725 23.581 1.00 0.00 C
ATOM 73 C ALA A 10 -4.504 4.426 24.799 1.00 0.00 C
ATOM 74 O ALA A 10 -4.317 4.997 25.875 1.00 0.00 O
ATOM 75 CB ALA A 10 -4.284 5.745 22.663 1.00 0.00 C
ATOM 76 N ALA A 11 -5.492 3.576 24.630 1.00 0.00 N
ATOM 77 CA ALA A 11 -6.434 3.220 25.719 1.00 0.00 C
ATOM 78 C ALA A 11 -5.661 2.490 26.818 1.00 0.00 C
ATOM 79 O ALA A 11 -5.909 2.684 28.009 1.00 0.00 O
ATOM 80 CB ALA A 11 -7.571 2.366 25.179 1.00 0.00 C
ATOM 81 N LEU A 12 -4.767 1.625 26.411 1.00 0.00 N
ATOM 82 CA LEU A 12 -3.966 0.808 27.355 1.00 0.00 C
ATOM 83 C LEU A 12 -3.062 1.739 28.164 1.00 0.00 C
ATOM 84 O LEU A 12 -2.852 1.540 29.362 1.00 0.00 O
ATOM 85 CB LEU A 12 -3.150 -0.241 26.597 1.00 0.00 C
ATOM 86 CG LEU A 12 -3.945 -1.362 25.925 1.00 0.00 C
ATOM 87 CD1 LEU A 12 -3.035 -2.228 25.068 1.00 0.00 C
ATOM 88 CD2 LEU A 12 -4.660 -2.212 26.964 1.00 0.00 C
ATOM 89 N LYS A 13 -2.505 2.729 27.483 1.00 0.00 N
ATOM 90 CA LYS A 13 -1.566 3.675 28.132 1.00 0.00 C
ATOM 91 C LYS A 13 -2.328 4.476 29.189 1.00 0.00 C
ATOM 92 O LYS A 13 -1.808 4.764 30.268 1.00 0.00 O
ATOM 93 CB LYS A 13 -0.926 4.595 27.090 1.00 0.00 C
ATOM 94 CD LYS A 13 0.644 4.863 25.151 1.00 0.00 C
ATOM 95 CE LYS A 13 1.630 4.165 24.228 1.00 0.00 C
ATOM 96 CG LYS A 13 0.058 3.896 26.166 1.00 0.00 C
ATOM 97 NZ LYS A 13 2.181 5.091 23.201 1.00 0.00 N
ATOM 98 N LYS A 14 -3.546 4.881 28.868 1.00 0.00 N
ATOM 99 CA LYS A 14 -4.372 5.694 29.793 1.00 0.00 C
ATOM 100 C LYS A 14 -4.696 4.854 31.029 1.00 0.00 C
ATOM 101 O LYS A 14 -4.711 5.355 32.155 1.00 0.00 O
ATOM 102 CB LYS A 14 -5.647 6.172 29.094 1.00 0.00 C
ATOM 103 CD LYS A 14 -6.713 7.640 27.360 1.00 0.00 C
ATOM 104 CE LYS A 14 -6.476 8.690 26.288 1.00 0.00 C
ATOM 105 CG LYS A 14 -5.409 7.220 28.020 1.00 0.00 C
ATOM 106 NZ LYS A 14 -7.740 9.079 25.603 1.00 0.00 N
ATOM 107 N GLU A 15 -5.004 3.599 30.823 1.00 0.00 N
ATOM 108 CA GLU A 15 -5.372 2.672 31.919 1.00 0.00 C
ATOM 109 C GLU A 15 -4.157 2.480 32.828 1.00 0.00 C
ATOM 110 O GLU A 15 -4.283 2.401 34.052 1.00 0.00 O
ATOM 111 CB GLU A 15 -5.860 1.338 31.351 1.00 0.00 C
ATOM 112 CD GLU A 15 -7.620 0.093 30.034 1.00 0.00 C
ATOM 113 CG GLU A 15 -7.198 1.420 30.635 1.00 0.00 C
ATOM 114 OE1 GLU A 15 -6.788 -0.838 30.008 1.00 0.00 O
ATOM 115 OE2 GLU A 15 -8.782 -0.015 29.590 1.00 0.00 O
ATOM 116 N ASN A 16 -3.001 2.367 32.210 1.00 0.00 N
ATOM 117 CA ASN A 16 -1.741 2.127 32.955 1.00 0.00 C
ATOM 118 C ASN A 16 -1.448 3.346 33.830 1.00 0.00 C
ATOM 119 O ASN A 16 -0.982 3.220 34.964 1.00 0.00 O
ATOM 120 CB ASN A 16 -0.594 1.830 31.987 1.00 0.00 C
ATOM 121 CG ASN A 16 0.676 1.409 32.699 1.00 0.00 C
ATOM 122 OD1 ASN A 16 1.667 2.140 32.706 1.00 0.00 O
ATOM 123 ND2 ASN A 16 0.650 0.227 33.303 1.00 0.00 N
ATOM 124 N ALA A 17 -1.685 4.532 33.281 1.00 0.00 N
ATOM 125 CA ALA A 17 -1.399 5.790 34.010 1.00 0.00 C
ATOM 126 C ALA A 17 -2.321 5.873 35.228 1.00 0.00 C
ATOM 127 O ALA A 17 -1.919 6.318 36.304 1.00 0.00 O
ATOM 128 CB ALA A 17 -1.583 6.988 33.092 1.00 0.00 C
ATOM 129 N ALA A 18 -3.570 5.496 35.059 1.00 0.00 N
ATOM 130 CA ALA A 18 -4.575 5.553 36.147 1.00 0.00 C
ATOM 131 C ALA A 18 -4.164 4.572 37.247 1.00 0.00 C
ATOM 132 O ALA A 18 -4.312 4.850 38.438 1.00 0.00 O
ATOM 133 CB ALA A 18 -5.960 5.233 35.607 1.00 0.00 C
ATOM 134 N LEU A 19 -3.698 3.419 36.840 1.00 0.00 N
ATOM 135 CA LEU A 19 -3.297 2.347 37.784 1.00 0.00 C
ATOM 136 C LEU A 19 -2.093 2.832 38.593 1.00 0.00 C
ATOM 137 O LEU A 19 -1.982 2.564 39.791 1.00 0.00 O
ATOM 138 CB LEU A 19 -2.977 1.057 37.026 1.00 0.00 C
ATOM 139 CG LEU A 19 -4.158 0.355 36.353 1.00 0.00 C
ATOM 140 CD1 LEU A 19 -3.676 -0.806 35.496 1.00 0.00 C
ATOM 141 CD2 LEU A 19 -5.156 -0.133 37.392 1.00 0.00 C
ATOM 142 N LYS A 20 -1.183 3.511 37.912 1.00 0.00 N
ATOM 143 CA LYS A 20 0.060 3.994 38.561 1.00 0.00 C
ATOM 144 C LYS A 20 -0.312 5.036 39.618 1.00 0.00 C
ATOM 145 O LYS A 20 0.280 5.088 40.697 1.00 0.00 O
ATOM 146 CB LYS A 20 1.018 4.574 37.519 1.00 0.00 C
ATOM 147 CD LYS A 20 3.292 5.495 36.988 1.00 0.00 C
ATOM 148 CE LYS A 20 4.623 5.957 37.557 1.00 0.00 C
ATOM 149 CG LYS A 20 2.349 5.036 38.088 1.00 0.00 C
ATOM 150 NZ LYS A 20 5.557 6.409 36.490 1.00 0.00 N
ATOM 151 N TRP A 21 -1.261 5.900 39.297 1.00 0.00 N
ATOM 152 CA TRP A 21 -1.686 6.978 40.222 1.00 0.00 C
ATOM 153 C TRP A 21 -2.323 6.342 41.458 1.00 0.00 C
ATOM 154 O TRP A 21 -2.134 6.806 42.583 1.00 0.00 O
ATOM 155 CB TRP A 21 -2.657 7.932 39.523 1.00 0.00 C
ATOM 156 CG TRP A 21 -3.108 9.068 40.388 1.00 0.00 C
ATOM 157 CD1 TRP A 21 -2.475 10.265 40.565 1.00 0.00 C
ATOM 158 NE1 TRP A 21 -3.190 11.056 41.432 1.00 0.00 N
ATOM 159 CD2 TRP A 21 -4.291 9.116 41.196 1.00 0.00 C
ATOM 160 CE2 TRP A 21 -4.310 10.370 41.833 1.00 0.00 C
ATOM 161 CH2 TRP A 21 -6.340 9.857 42.923 1.00 0.00 C
ATOM 162 CZ2 TRP A 21 -5.332 10.752 42.700 1.00 0.00 C
ATOM 163 CE3 TRP A 21 -5.335 8.220 41.442 1.00 0.00 C
ATOM 164 CZ3 TRP A 21 -6.347 8.603 42.302 1.00 0.00 C
ATOM 165 N GLU A 22 -3.114 5.320 41.251 1.00 0.00 N
ATOM 166 CA GLU A 22 -3.826 4.621 42.348 1.00 0.00 C
ATOM 167 C GLU A 22 -2.794 3.954 43.257 1.00 0.00 C
ATOM 168 O GLU A 22 -2.940 3.932 44.481 1.00 0.00 O
ATOM 169 CB GLU A 22 -4.812 3.598 41.780 1.00 0.00 C
ATOM 170 CD GLU A 22 -6.925 3.172 40.464 1.00 0.00 C
ATOM 171 CG GLU A 22 -6.003 4.215 41.065 1.00 0.00 C
ATOM 172 OE1 GLU A 22 -6.542 1.984 40.438 1.00 0.00 O
ATOM 173 OE2 GLU A 22 -8.032 3.544 40.020 1.00 0.00 O
ATOM 174 N ILE A 23 -1.782 3.381 42.639 1.00 0.00 N
ATOM 175 CA ILE A 23 -0.729 2.650 43.384 1.00 0.00 C
ATOM 176 C ILE A 23 0.034 3.646 44.259 1.00 0.00 C
ATOM 177 O ILE A 23 0.409 3.341 45.393 1.00 0.00 O
ATOM 178 CB ILE A 23 0.223 1.904 42.430 1.00 0.00 C
ATOM 179 CD1 ILE A 23 0.322 -0.186 43.886 1.00 0.00 C
ATOM 180 CG1 ILE A 23 1.099 0.923 43.211 1.00 0.00 C
ATOM 181 CG2 ILE A 23 1.055 2.893 41.628 1.00 0.00 C
ATOM 182 N ALA A 24 0.298 4.826 43.710 1.00 0.00 N
ATOM 183 CA ALA A 24 1.070 5.860 44.439 1.00 0.00 C
ATOM 184 C ALA A 24 0.261 6.309 45.657 1.00 0.00 C
ATOM 185 O ALA A 24 0.810 6.553 46.733 1.00 0.00 O
ATOM 186 CB ALA A 24 1.387 7.030 43.521 1.00 0.00 C
ATOM 187 N ALA A 25 -1.033 6.472 45.488 1.00 0.00 N
ATOM 188 CA ALA A 25 -1.929 6.931 46.576 1.00 0.00 C
ATOM 189 C ALA A 25 -1.951 5.868 47.676 1.00 0.00 C
ATOM 190 O ALA A 25 -1.974 6.183 48.867 1.00 0.00 O
ATOM 191 CB ALA A 25 -3.325 7.199 46.035 1.00 0.00 C
ATOM 192 N LEU A 26 -1.993 4.625 47.269 1.00 0.00 N
ATOM 193 CA LEU A 26 -2.061 3.483 48.212 1.00 0.00 C
ATOM 194 C LEU A 26 -0.765 3.437 49.022 1.00 0.00 C
ATOM 195 O LEU A 26 -0.771 3.148 50.220 1.00 0.00 O
ATOM 196 CB LEU A 26 -2.290 2.174 47.453 1.00 0.00 C
ATOM 197 CG LEU A 26 -3.655 2.011 46.780 1.00 0.00 C
ATOM 198 CD1 LEU A 26 -3.685 0.755 45.923 1.00 0.00 C
ATOM 199 CD2 LEU A 26 -4.765 1.969 47.819 1.00 0.00 C
ATOM 200 N LYS A 27 0.343 3.689 48.341 1.00 0.00 N
ATOM 201 CA LYS A 27 1.675 3.627 48.990 1.00 0.00 C
ATOM 202 C LYS A 27 1.758 4.729 50.047 1.00 0.00 C
ATOM 203 O LYS A 27 2.320 4.537 51.126 1.00 0.00 O
ATOM 204 CB LYS A 27 2.786 3.770 47.948 1.00 0.00 C
ATOM 205 CD LYS A 27 4.039 2.785 46.008 1.00 0.00 C
ATOM 206 CE LYS A 27 4.182 1.586 45.086 1.00 0.00 C
ATOM 207 CG LYS A 27 2.928 2.571 47.024 1.00 0.00 C
ATOM 208 NZ LYS A 27 5.238 1.799 44.058 1.00 0.00 N
ATOM 209 N GLN A 28 1.241 5.905 49.726 1.00 0.00 N
ATOM 210 CA GLN A 28 1.290 7.063 50.651 1.00 0.00 C
ATOM 211 C GLN A 28 0.449 6.739 51.887 1.00 0.00 C
ATOM 212 O GLN A 28 0.811 7.086 53.012 1.00 0.00 O
ATOM 213 CB GLN A 28 0.790 8.329 49.952 1.00 0.00 C
ATOM 214 CD GLN A 28 3.046 9.053 49.078 1.00 0.00 C
ATOM 215 CG GLN A 28 1.606 8.729 48.734 1.00 0.00 C
ATOM 216 OE1 GLN A 28 3.321 10.012 49.799 1.00 0.00 O
ATOM 217 NE2 GLN A 28 3.971 8.253 48.562 1.00 0.00 N
TER
ATOM 218 N GLU B 1 -1.891 -5.868 52.981 1.00 0.00 N
ATOM 219 CA GLU B 1 -2.738 -5.341 51.885 1.00 0.00 C
ATOM 220 C GLU B 1 -1.874 -4.465 50.975 1.00 0.00 C
ATOM 221 O GLU B 1 -2.022 -4.476 49.752 1.00 0.00 O
ATOM 222 CB GLU B 1 -3.923 -4.557 52.453 1.00 0.00 C
ATOM 223 CD GLU B 1 -6.083 -4.603 53.761 1.00 0.00 C
ATOM 224 CG GLU B 1 -4.965 -5.421 53.144 1.00 0.00 C
ATOM 225 OE1 GLU B 1 -5.951 -3.362 53.816 1.00 0.00 O
ATOM 226 OE2 GLU B 1 -7.091 -5.204 54.190 1.00 0.00 O
ATOM 227 N ILE B 2 -1.011 -3.687 51.593 1.00 0.00 N
ATOM 228 CA ILE B 2 -0.141 -2.745 50.849 1.00 0.00 C
ATOM 229 C ILE B 2 0.819 -3.552 49.973 1.00 0.00 C
ATOM 230 O ILE B 2 1.119 -3.173 48.839 1.00 0.00 O
ATOM 231 CB ILE B 2 0.627 -1.812 51.804 1.00 0.00 C
ATOM 232 CD1 ILE B 2 0.288 -0.100 53.661 1.00 0.00 C
ATOM 233 CG1 ILE B 2 -0.339 -0.865 52.517 1.00 0.00 C
ATOM 234 CG2 ILE B 2 1.711 -1.055 51.051 1.00 0.00 C
ATOM 235 N ALA B 3 1.333 -4.646 50.523 1.00 0.00 N
ATOM 236 CA ALA B 3 2.311 -5.489 49.794 1.00 0.00 C
ATOM 237 C ALA B 3 1.618 -6.103 48.576 1.00 0.00 C
ATOM 238 O ALA B 3 2.207 -6.223 47.500 1.00 0.00 O
ATOM 239 CB ALA B 3 2.874 -6.563 50.713 1.00 0.00 C
ATOM 240 N ALA B 4 0.390 -6.542 48.745 1.00 0.00 N
ATOM 241 CA ALA B 4 -0.385 -7.185 47.657 1.00 0.00 C
ATOM 242 C ALA B 4 -0.637 -6.152 46.557 1.00 0.00 C
ATOM 243 O ALA B 4 -0.591 -6.464 45.366 1.00 0.00 O
ATOM 244 CB ALA B 4 -1.690 -7.750 48.198 1.00 0.00 C
ATOM 245 N LEU B 5 -0.947 -4.947 46.964 1.00 0.00 N
ATOM 246 CA LEU B 5 -1.262 -3.848 46.020 1.00 0.00 C
ATOM 247 C LEU B 5 -0.006 -3.522 45.210 1.00 0.00 C
ATOM 248 O LEU B 5 -0.074 -3.241 44.012 1.00 0.00 O
ATOM 249 CB LEU B 5 -1.771 -2.620 46.778 1.00 0.00 C
ATOM 250 CG LEU B 5 -3.138 -2.757 47.451 1.00 0.00 C
ATOM 251 CD1 LEU B 5 -3.441 -1.537 48.307 1.00 0.00 C
ATOM 252 CD2 LEU B 5 -4.231 -2.959 46.412 1.00 0.00 C
ATOM 253 N LYS B 6 1.131 -3.527 45.892 1.00 0.00 N
ATOM 254 CA LYS B 6 2.417 -3.178 45.243 1.00 0.00 C
ATOM 255 C LYS B 6 2.737 -4.237 44.186 1.00 0.00 C
ATOM 256 O LYS B 6 3.244 -3.927 43.106 1.00 0.00 O
ATOM 257 CB LYS B 6 3.533 -3.076 46.285 1.00 0.00 C
ATOM 258 CD LYS B 6 4.542 -1.842 48.224 1.00 0.00 C
ATOM 259 CE LYS B 6 4.422 -0.640 49.146 1.00 0.00 C
ATOM 260 CG LYS B 6 3.411 -1.875 47.209 1.00 0.00 C
ATOM 261 NZ LYS B 6 5.499 -0.618 50.173 1.00 0.00 N
ATOM 262 N GLN B 7 2.487 -5.496 44.507 1.00 0.00 N
ATOM 263 CA GLN B 7 2.786 -6.616 43.582 1.00 0.00 C
ATOM 264 C GLN B 7 1.895 -6.483 42.346 1.00 0.00 C
ATOM 265 O GLN B 7 2.323 -6.744 41.221 1.00 0.00 O
ATOM 266 CB GLN B 7 2.572 -7.960 44.281 1.00 0.00 C
ATOM 267 CD GLN B 7 3.298 -9.561 46.095 1.00 0.00 C
ATOM 268 CG GLN B 7 3.587 -8.261 45.372 1.00 0.00 C
ATOM 269 OE1 GLN B 7 2.153 -10.011 46.149 1.00 0.00 O
ATOM 270 NE2 GLN B 7 4.337 -10.170 46.654 1.00 0.00 N
ATOM 271 N GLU B 8 0.652 -6.130 42.552 1.00 0.00 N
ATOM 272 CA GLU B 8 -0.336 -5.992 41.456 1.00 0.00 C
ATOM 273 C GLU B 8 0.098 -4.842 40.546 1.00 0.00 C
ATOM 274 O GLU B 8 -0.033 -4.912 39.323 1.00 0.00 O
ATOM 275 CB GLU B 8 -1.737 -5.755 42.024 1.00 0.00 C
ATOM 276 CD GLU B 8 -3.689 -6.668 43.342 1.00 0.00 C
ATOM 277 CG GLU B 8 -2.327 -6.958 42.741 1.00 0.00 C
ATOM 278 OE1 GLU B 8 -4.087 -5.484 43.367 1.00 0.00 O
ATOM 279 OE2 GLU B 8 -4.357 -7.624 43.788 1.00 0.00 O
ATOM 280 N ILE B 9 0.571 -3.780 41.164 1.00 0.00 N
ATOM 281 CA ILE B 9 0.985 -2.566 40.420 1.00 0.00 C
ATOM 282 C ILE B 9 2.190 -2.914 39.544 1.00 0.00 C
ATOM 283 O ILE B 9 2.310 -2.447 38.410 1.00 0.00 O
ATOM 284 CB ILE B 9 1.309 -1.402 41.375 1.00 0.00 C
ATOM 285 CD1 ILE B 9 0.149 0.341 39.921 1.00 0.00 C
ATOM 286 CG1 ILE B 9 1.432 -0.091 40.595 1.00 0.00 C
ATOM 287 CG2 ILE B 9 2.566 -1.705 42.176 1.00 0.00 C
ATOM 288 N ALA B 10 3.103 -3.706 40.094 1.00 0.00 N
ATOM 289 CA ALA B 10 4.339 -4.079 39.365 1.00 0.00 C
ATOM 290 C ALA B 10 3.955 -4.922 38.147 1.00 0.00 C
ATOM 291 O ALA B 10 4.541 -4.792 37.071 1.00 0.00 O
ATOM 292 CB ALA B 10 5.290 -4.831 40.284 1.00 0.00 C
ATOM 293 N ALA B 11 3.010 -5.821 38.316 1.00 0.00 N
ATOM 294 CA ALA B 11 2.563 -6.724 37.228 1.00 0.00 C
ATOM 295 C ALA B 11 1.913 -5.882 36.128 1.00 0.00 C
ATOM 296 O ALA B 11 2.082 -6.148 34.937 1.00 0.00 O
ATOM 297 CB ALA B 11 1.601 -7.770 37.769 1.00 0.00 C
ATOM 298 N LEU B 12 1.141 -4.906 36.535 1.00 0.00 N
ATOM 299 CA LEU B 12 0.408 -4.029 35.591 1.00 0.00 C
ATOM 300 C LEU B 12 1.424 -3.222 34.781 1.00 0.00 C
ATOM 301 O LEU B 12 1.247 -2.993 33.583 1.00 0.00 O
ATOM 302 CB LEU B 12 -0.555 -3.113 36.349 1.00 0.00 C
ATOM 303 CG LEU B 12 -1.749 -3.792 37.021 1.00 0.00 C
ATOM 304 CD1 LEU B 12 -2.521 -2.799 37.877 1.00 0.00 C
ATOM 305 CD2 LEU B 12 -2.666 -4.419 35.982 1.00 0.00 C
ATOM 306 N LYS B 13 2.464 -2.765 35.463 1.00 0.00 N
ATOM 307 CA LYS B 13 3.499 -1.924 34.814 1.00 0.00 C
ATOM 308 C LYS B 13 4.220 -2.762 33.757 1.00 0.00 C
ATOM 309 O LYS B 13 4.558 -2.274 32.677 1.00 0.00 O
ATOM 310 CB LYS B 13 4.478 -1.379 35.856 1.00 0.00 C
ATOM 311 CD LYS B 13 4.901 0.157 37.796 1.00 0.00 C
ATOM 312 CE LYS B 13 4.304 1.207 38.718 1.00 0.00 C
ATOM 313 CG LYS B 13 3.880 -0.331 36.781 1.00 0.00 C
ATOM 314 NZ LYS B 13 5.280 1.663 39.746 1.00 0.00 N
ATOM 315 N LYS B 14 4.503 -4.015 34.078 1.00 0.00 N
ATOM 316 CA LYS B 14 5.230 -4.917 33.153 1.00 0.00 C
ATOM 317 C LYS B 14 4.362 -5.157 31.917 1.00 0.00 C
ATOM 318 O LYS B 14 4.859 -5.221 30.792 1.00 0.00 O
ATOM 319 CB LYS B 14 5.580 -6.232 33.852 1.00 0.00 C
ATOM 320 CD LYS B 14 6.936 -7.439 35.585 1.00 0.00 C
ATOM 321 CE LYS B 14 8.005 -7.307 36.657 1.00 0.00 C
ATOM 322 CG LYS B 14 6.647 -6.100 34.926 1.00 0.00 C
ATOM 323 NZ LYS B 14 8.268 -8.602 37.342 1.00 0.00 N
ATOM 324 N GLU B 15 3.083 -5.339 32.123 1.00 0.00 N
ATOM 325 CA GLU B 15 2.124 -5.613 31.027 1.00 0.00 C
ATOM 326 C GLU B 15 2.054 -4.386 30.117 1.00 0.00 C
ATOM 327 O GLU B 15 1.963 -4.503 28.894 1.00 0.00 O
ATOM 328 CB GLU B 15 0.747 -5.965 31.595 1.00 0.00 C
ATOM 329 CD GLU B 15 -0.667 -7.591 32.912 1.00 0.00 C
ATOM 330 CG GLU B 15 0.695 -7.304 32.311 1.00 0.00 C
ATOM 331 OE1 GLU B 15 -1.510 -6.670 32.938 1.00 0.00 O
ATOM 332 OE2 GLU B 15 -0.891 -8.736 33.357 1.00 0.00 O
ATOM 333 N ASN B 16 2.056 -3.223 30.735 1.00 0.00 N
ATOM 334 CA ASN B 16 1.941 -1.946 29.991 1.00 0.00 C
ATOM 335 C ASN B 16 3.183 -1.775 29.115 1.00 0.00 C
ATOM 336 O ASN B 16 3.104 -1.299 27.982 1.00 0.00 O
ATOM 337 CB ASN B 16 1.760 -0.776 30.960 1.00 0.00 C
ATOM 338 CG ASN B 16 1.465 0.530 30.248 1.00 0.00 C
ATOM 339 OD1 ASN B 16 2.290 1.444 30.241 1.00 0.00 O
ATOM 340 ND2 ASN B 16 0.286 0.621 29.645 1.00 0.00 N
ATOM 341 N ALA B 17 4.340 -2.128 29.665 1.00 0.00 N
ATOM 342 CA ALA B 17 5.621 -1.969 28.936 1.00 0.00 C
ATOM 343 C ALA B 17 5.611 -2.895 27.718 1.00 0.00 C
ATOM 344 O ALA B 17 6.095 -2.538 26.642 1.00 0.00 O
ATOM 345 CB ALA B 17 6.795 -2.272 29.854 1.00 0.00 C
ATOM 346 N ALA B 18 5.113 -4.100 27.887 1.00 0.00 N
ATOM 347 CA ALA B 18 5.070 -5.106 26.799 1.00 0.00 C
ATOM 348 C ALA B 18 4.135 -4.600 25.699 1.00 0.00 C
ATOM 349 O ALA B 18 4.397 -4.775 24.508 1.00 0.00 O
ATOM 350 CB ALA B 18 4.614 -6.452 27.340 1.00 0.00 C
ATOM 351 N LEU B 19 3.033 -4.022 26.106 1.00 0.00 N
ATOM 352 CA LEU B 19 2.007 -3.517 25.162 1.00 0.00 C
ATOM 353 C LEU B 19 2.608 -2.367 24.352 1.00 0.00 C
ATOM 354 O LEU B 19 2.354 -2.229 23.154 1.00 0.00 O
ATOM 355 CB LEU B 19 0.755 -3.070 25.920 1.00 0.00 C
ATOM 356 CG LEU B 19 -0.061 -4.176 26.592 1.00 0.00 C
ATOM 357 CD1 LEU B 19 -1.169 -3.581 27.449 1.00 0.00 C
ATOM 358 CD2 LEU B 19 -0.645 -5.120 25.553 1.00 0.00 C
ATOM 359 N LYS B 20 3.374 -1.528 25.034 1.00 0.00 N
ATOM 360 CA LYS B 20 3.979 -0.340 24.385 1.00 0.00 C
ATOM 361 C LYS B 20 4.978 -0.813 23.328 1.00 0.00 C
ATOM 362 O LYS B 20 5.089 -0.229 22.248 1.00 0.00 O
ATOM 363 CB LYS B 20 4.653 0.555 25.427 1.00 0.00 C
ATOM 364 CD LYS B 20 5.797 2.725 25.958 1.00 0.00 C
ATOM 365 CE LYS B 20 6.390 4.003 25.388 1.00 0.00 C
ATOM 366 CG LYS B 20 5.246 1.833 24.857 1.00 0.00 C
ATOM 367 NZ LYS B 20 6.934 4.887 26.456 1.00 0.00 N
ATOM 368 N TRP B 21 5.744 -1.843 23.649 1.00 0.00 N
ATOM 369 CA TRP B 21 6.775 -2.373 22.725 1.00 0.00 C
ATOM 370 C TRP B 21 6.079 -2.944 21.488 1.00 0.00 C
ATOM 371 O TRP B 21 6.560 -2.801 20.363 1.00 0.00 O
ATOM 372 CB TRP B 21 7.627 -3.434 23.425 1.00 0.00 C
ATOM 373 CG TRP B 21 8.714 -3.996 22.560 1.00 0.00 C
ATOM 374 CD1 TRP B 21 9.968 -3.485 22.385 1.00 0.00 C
ATOM 375 NE1 TRP B 21 10.684 -4.274 21.518 1.00 0.00 N
ATOM 376 CD2 TRP B 21 8.644 -5.178 21.753 1.00 0.00 C
ATOM 377 CE2 TRP B 21 9.891 -5.321 21.117 1.00 0.00 C
ATOM 378 CH2 TRP B 21 9.179 -7.290 20.027 1.00 0.00 C
ATOM 379 CZ2 TRP B 21 10.170 -6.376 20.250 1.00 0.00 C
ATOM 380 CE3 TRP B 21 7.649 -6.128 21.506 1.00 0.00 C
ATOM 381 CZ3 TRP B 21 7.930 -7.172 20.646 1.00 0.00 C
ATOM 382 N GLU B 22 4.984 -3.629 21.694 1.00 0.00 N
ATOM 383 CA GLU B 22 4.218 -4.269 20.598 1.00 0.00 C
ATOM 384 C GLU B 22 3.656 -3.175 19.688 1.00 0.00 C
ATOM 385 O GLU B 22 3.620 -3.319 18.465 1.00 0.00 O
ATOM 386 CB GLU B 22 3.103 -5.149 21.166 1.00 0.00 C
ATOM 387 CD GLU B 22 2.470 -7.208 22.484 1.00 0.00 C
ATOM 388 CG GLU B 22 3.599 -6.394 21.883 1.00 0.00 C
ATOM 389 OE1 GLU B 22 1.326 -6.709 22.510 1.00 0.00 O
ATOM 390 OE2 GLU B 22 2.730 -8.346 22.930 1.00 0.00 O
ATOM 391 N ILE B 23 3.186 -2.112 20.306 1.00 0.00 N
ATOM 392 CA ILE B 23 2.563 -0.991 19.562 1.00 0.00 C
ATOM 393 C ILE B 23 3.630 -0.331 18.686 1.00 0.00 C
ATOM 394 O ILE B 23 3.364 0.072 17.553 1.00 0.00 O
ATOM 395 CB ILE B 23 1.917 0.030 20.517 1.00 0.00 C
ATOM 396 CD1 ILE B 23 -0.154 0.338 19.063 1.00 0.00 C
ATOM 397 CG1 ILE B 23 1.027 1.000 19.737 1.00 0.00 C
ATOM 398 CG2 ILE B 23 2.985 0.760 21.318 1.00 0.00 C
ATOM 399 N ALA B 24 4.830 -0.185 19.236 1.00 0.00 N
ATOM 400 CA ALA B 24 5.936 0.481 18.507 1.00 0.00 C
ATOM 401 C ALA B 24 6.303 -0.370 17.289 1.00 0.00 C
ATOM 402 O ALA B 24 6.600 0.152 16.213 1.00 0.00 O
ATOM 403 CB ALA B 24 7.132 0.681 19.426 1.00 0.00 C
ATOM 404 N ALA B 25 6.337 -1.673 17.458 1.00 0.00 N
ATOM 405 CA ALA B 25 6.705 -2.610 16.370 1.00 0.00 C
ATOM 406 C ALA B 25 5.645 -2.527 15.270 1.00 0.00 C
ATOM 407 O ALA B 25 5.956 -2.581 14.079 1.00 0.00 O
ATOM 408 CB ALA B 25 6.834 -4.026 16.911 1.00 0.00 C
ATOM 409 N LEU B 26 4.404 -2.445 15.677 1.00 0.00 N
ATOM 410 CA LEU B 26 3.261 -2.400 14.733 1.00 0.00 C
ATOM 411 C LEU B 26 3.344 -1.105 13.923 1.00 0.00 C
ATOM 412 O LEU B 26 3.056 -1.083 12.725 1.00 0.00 O
ATOM 413 CB LEU B 26 1.936 -2.499 15.491 1.00 0.00 C
ATOM 414 CG LEU B 26 1.638 -3.841 16.164 1.00 0.00 C
ATOM 415 CD1 LEU B 26 0.385 -3.747 17.020 1.00 0.00 C
ATOM 416 CD2 LEU B 26 1.488 -4.942 15.125 1.00 0.00 C
ATOM 417 N LYS B 27 3.704 -0.028 14.605 1.00 0.00 N
ATOM 418 CA LYS B 27 3.774 1.303 13.956 1.00 0.00 C
ATOM 419 C LYS B 27 4.880 1.277 12.899 1.00 0.00 C
ATOM 420 O LYS B 27 4.744 1.855 11.819 1.00 0.00 O
ATOM 421 CB LYS B 27 4.025 2.395 14.998 1.00 0.00 C
ATOM 422 CD LYS B 27 3.168 3.739 16.937 1.00 0.00 C
ATOM 423 CE LYS B 27 1.988 4.000 17.859 1.00 0.00 C
ATOM 424 CG LYS B 27 2.846 2.654 15.922 1.00 0.00 C
ATOM 425 NZ LYS B 27 2.303 5.030 18.886 1.00 0.00 N
ATOM 426 N GLN B 28 5.998 0.646 13.220 1.00 0.00 N
ATOM 427 CA GLN B 28 7.155 0.580 12.296 1.00 0.00 C
ATOM 428 C GLN B 28 6.750 -0.225 11.059 1.00 0.00 C
ATOM 429 O GLN B 28 7.132 0.101 9.934 1.00 0.00 O
ATOM 430 CB GLN B 28 8.364 -0.044 12.996 1.00 0.00 C
ATOM 431 CD GLN B 28 9.309 2.130 13.870 1.00 0.00 C
ATOM 432 CG GLN B 28 8.843 0.729 14.214 1.00 0.00 C
ATOM 433 OE1 GLN B 28 10.291 2.308 13.149 1.00 0.00 O
ATOM 434 NE2 GLN B 28 8.604 3.130 14.386 1.00 0.00 N
TER
END
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