{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "\n", "*This notebook contains material from [PyRosetta](https://RosettaCommons.github.io/PyRosetta.notebooks);\n", "content is available [on Github](https://github.com/RosettaCommons/PyRosetta.notebooks.git).*" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\n", "< [Side Chain Conformations and Dunbrack Energies](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.01-Side-Chain-Conformations-and-Dunbrack-Energies.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.03-Design-with-a-resfile-and-relax.ipynb) >

\"Open" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Packing and Relax\n", "Keywords: PackRotamersMover, FastRelax, MoveMapFactory, cartesian, ResidueSelector, NeighborhoodResidueSelector, CDRResidueSelector, TaskFactory, TaskOperation, InitializeFromCommandline, RestrictToRepacking, PreventRepackingRLT, OperateOnResidueSubsetOperation, SimpleMetric, SequenceMetric, clone()\n", "\n", "## Overview\n", "Here, you will learn how to optimize the side-chains of a protein. In Rosetta, we call this `packing`. We will use TaskFactories to control which residues are optimized. We will use this knowledge to refine a specific region of a protein. In the next workshop, we will use what we learned here to begin designing proteins." ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "!pip install pyrosettacolabsetup\n", "import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()\n", "import pyrosetta; pyrosetta.init()\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "**Make sure you are in the directory with the pdb files:**\n", "\n", "`cd google_drive/MyDrive/student-notebooks/`" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Imports\n", "\n", "Before we begin, we must import some specific machinery from Rosetta. Much of these tools are automatically imported when we do `from pyrosetta import *`, however, some are not. You should get into the habit of importing everything you need. This will get you comfortable with the organization of Rosetta and make it easier to find tools that are beyond the scope of these workshops." ] }, { "cell_type": "code", "execution_count": 29, "metadata": {}, "outputs": [], "source": [ "#Python\n", "from pyrosetta import *\n", "from pyrosetta.rosetta import *\n", "from pyrosetta.teaching import *\n", "\n", "#Core Includes\n", "from rosetta.core.kinematics import MoveMap\n", "from rosetta.core.kinematics import FoldTree\n", "from rosetta.core.pack.task import TaskFactory\n", "from rosetta.core.pack.task import operation\n", "from rosetta.core.simple_metrics import metrics\n", "from rosetta.core.select import residue_selector as selections\n", "from rosetta.core import select\n", "from rosetta.core.select.movemap import *\n", "\n", "#Protocol Includes\n", "from rosetta.protocols import minimization_packing as pack_min\n", "from rosetta.protocols import relax as rel\n", "from rosetta.protocols.antibody.residue_selector import CDRResidueSelector\n", "from rosetta.protocols.antibody import *\n", "from rosetta.protocols.loops import *\n", "from rosetta.protocols.relax import FastRelax\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Intitlialization \n", "\n", "Here, we will use command-line options to set the relax rounds to 2 instead of default 5 for speed of demo. This is a bit tricky to do in code.\n", "We also set the input antibody numbering scheme so that Rosetta understands the nomenclature of our antibody. \n", "\n", "\n", "Note that typically, we would add these options: `-ex1` and `-ex2` in order to increase the amount of rotamers\n", " available for packing, but this will slow us down for the demo, so we are keeping this out." ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0mcore.init: \u001b[0mChecking for fconfig files in pwd and ./rosetta/flags\n", "\u001b[0mcore.init: \u001b[0mReading fconfig.../Users/jadolfbr/.rosetta/flags/common\n", "\u001b[0mcore.init: \u001b[0m\n", "\u001b[0mcore.init: \u001b[0m\n", "\u001b[0mcore.init: \u001b[0mRosetta version: PyRosetta4.Release.python27.mac r206 2019.01+release.dbc838b6ae6 dbc838b6ae620b1293476b1bd4366ffc2facc5b5 http://www.pyrosetta.org 2019-01-03T10:31:13\n", "\u001b[0mcore.init: \u001b[0mcommand: PyRosetta -use_input_sc -input_ab_scheme AHo_Scheme -ignore_unrecognized_res -ignore_zero_occupancy false -load_PDB_components false -relax:default_repeats 2 -database /Library/Python/2.7/site-packages/pyrosetta-2019.1+release.dbc838b6ae6-py2.7-macosx-10.13-intel.egg/pyrosetta/database\n", "\u001b[0mcore.init: \u001b[0m'RNG device' seed mode, using '/dev/urandom', seed=-153595891 seed_offset=0 real_seed=-153595891\n", "\u001b[0mcore.init.random: \u001b[0mRandomGenerator:init: Normal mode, seed=-153595891 RG_type=mt19937\n" ] } ], "source": [ "init('-use_input_sc -input_ab_scheme AHo_Scheme -ignore_unrecognized_res \\\n", " -ignore_zero_occupancy false -load_PDB_components false -relax:default_repeats 2 -no_fconfig')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Import and copy pose\n", "\n", "Begin by importing a pose. Here, we are going to use an antibody from the PDB. \n", "Note that we use the clone function to copy the pose into `original_pose`. Using the equal sign will only make what is known as a shallow copy in python and anything we do to pose will be seen in original_pose. The clone operation copies all the data into the original_pose and is the Rosetta equivalent of the python module, `copy.deep_copy`. " ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0mcore.chemical.GlobalResidueTypeSet: \u001b[0mFinished initializing fa_standard residue type set. Created 636 residue types\n", "\u001b[0mcore.chemical.GlobalResidueTypeSet: \u001b[0mTotal time to initialize 0.76167 seconds.\n", "\u001b[0mcore.import_pose.import_pose: \u001b[0mFile '2r0l_1_1.pdb' automatically determined to be of type PDB\n", "\u001b[0mcore.io.pdb.pdb_reader: \u001b[0mParsing 0 .pdb records with unknown format to search for Rosetta-specific comments.\n", "\u001b[0mcore.conformation.Conformation: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m missing heavyatom: OXT on residue ARG:CtermProteinFull 108\n", "\u001b[0mcore.conformation.Conformation: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m missing heavyatom: OXT on residue SER:CtermProteinFull 225\n", "\u001b[0mcore.conformation.Conformation: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m missing heavyatom: OXT on residue ARG:CtermProteinFull 464\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mFound disulfide between residues 23 88\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 23 CYS\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 88 CYS\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 23 CYD\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 88 CYD\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mFound disulfide between residues 130 204\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 130 CYS\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 204 CYS\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 130 CYD\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 204 CYD\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mFound disulfide between residues 250 266\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 250 CYS\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 266 CYS\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 250 CYD\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 266 CYD\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mFound disulfide between residues 258 328\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 258 CYS\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 328 CYS\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 258 CYD\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 328 CYD\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mFound disulfide between residues 353 422\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 353 CYS\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 422 CYS\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 353 CYD\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 422 CYD\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mFound disulfide between residues 385 401\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 385 CYS\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 401 CYS\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 385 CYD\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 401 CYD\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mFound disulfide between residues 412 440\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 412 CYS\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 440 CYS\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 412 CYD\n", "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 440 CYD\n" ] } ], "source": [ "#Import a pose\n", "pose = pose_from_pdb(\"inputs/2r0l_1_1.pdb\")\n", "original_pose = pose.clone()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Setup a Normal TaskFactory\n", "\n", "A `TaskFactory` is what we use to control packing specific residues in a pose. We first pass InitializeFromCommandLine which uses any of the options specified in the `pyrosetta.init()` function.\n", "\n", "The `TaskFactory` is made up of a list of `TaskOperations`. These Taskops make up the bread and butter of controlling packing (and subsequently design). The taskops can be given to factory in any order. \n", "\n", "In Rosetta, ALL residues are set to both pack AND design by default. We use taskops to turn things off, like creating an ice sculpture. Here, we turn design off by using the `RestrictToRepacking` operation." ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "scrolled": true }, "outputs": [], "source": [ "tf = TaskFactory()\n", "tf.push_back(operation.InitializeFromCommandline())\n", "tf.push_back(operation.RestrictToRepacking())" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Setup The Packer\n", "\n", "Here, we setup the packer and pass the TaskFactory to it. In general, if something can be packed, it will accept a TaskFactory. Every time the protein is packed for a single round, the TaskFactory will generate what is called the PackerTask. This object has all of the instructions needed for Rosetta to do packing and design. Some TaskOperations can respond to environmental changes in the pose, such as neighboring residues and dynamically change at each packing step. This is one of the reasons we use the TaskFactory machinery to setup packing instead of hacking the PackerTask itself as has been done in some of the earlier tutorials you may see on the web. " ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0mprotocols.minimization_packing.PackRotamersMover: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m undefined ScoreFunction -- creating a default one\n", "\u001b[0mcore.scoring.ScoreFunctionFactory: \u001b[0mSCOREFUNCTION: \u001b[32mref2015\u001b[0m\n", "\u001b[0mcore.scoring.etable: \u001b[0mStarting energy table calculation\n", "\u001b[0mcore.scoring.etable: \u001b[0msmooth_etable: changing atr/rep split to bottom of energy well\n", "\u001b[0mcore.scoring.etable: \u001b[0msmooth_etable: spline smoothing lj etables (maxdis = 6)\n", "\u001b[0mcore.scoring.etable: \u001b[0msmooth_etable: spline smoothing solvation etables (max_dis = 6)\n", "\u001b[0mcore.scoring.etable: \u001b[0mFinished calculating energy tables.\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/rama/fd/all.ramaProb\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/rama/fd/prepro.ramaProb\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/omega/omega_ppdep.all.txt\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/P_AA_pp/P_AA\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/P_AA_pp/P_AA_n\n", "\u001b[0mcore.scoring.P_AA: \u001b[0mshapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/elec_cp_reps.dat\n", "\u001b[0mcore.scoring.elec.util: \u001b[0mRead 40 countpair representative atoms\n", "\u001b[0mcore.pack.dunbrack.RotamerLibrary: \u001b[0mshapovalov_lib_fixes_enable option is true.\n", "\u001b[0mcore.pack.dunbrack.RotamerLibrary: \u001b[0mshapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\n", "\u001b[0mcore.pack.dunbrack.RotamerLibrary: \u001b[0mBinary rotamer library selected: /Library/Python/2.7/site-packages/pyrosetta-2019.1+release.dbc838b6ae6-py2.7-macosx-10.13-intel.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\n", "\u001b[0mcore.pack.dunbrack.RotamerLibrary: \u001b[0mUsing Dunbrack library binary file '/Library/Python/2.7/site-packages/pyrosetta-2019.1+release.dbc838b6ae6-py2.7-macosx-10.13-intel.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\n", "\u001b[0mcore.pack.dunbrack.RotamerLibrary: \u001b[0mDunbrack 2010 library took 0.249423 seconds to load from binary\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 18337 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n" ] }, { "data": { "text/plain": [ "True" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "packer = pack_min.PackRotamersMover()\n", "packer.task_factory(tf)\n", "\n", "#Note that we are not passing a scorefunction here. We will use the default, cmd-line scorefunction, \n", "# which is accessed through rosetta.core.scoring.get_score_function() and part of the packer. We use use a scorefunction later. \n", "\n", "#Run the packer. (Note this may take a few minutes)\n", "#Skip for tests\n", "if not os.getenv(\"DEBUG\"):\n", " packer.apply(pose)\n", "\n", "#Dump the PDB\n", "pose.dump_pdb('/outputs/2r0l_all_repack.pdb')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Lets compare the energies of the before and after pose. Any difference?" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0mcore.scoring.ScoreFunctionFactory: \u001b[0mSCOREFUNCTION: \u001b[32mref2015\u001b[0m\n" ] } ], "source": [ "\n", "scorefxn = get_score_function()\n", "before = scorefxn.score(original_pose)\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Check the sequence of the pose and the original pose using either the `SequenceMetric` \n", " `rosetta.core.simple_metrics.metrics.SequenceMetric` (and it's calculate function) OR directly using the pose's `.sequence()` function. \n", " Make sure that the poses have the same sequence - as packing is just design using single residue rotamers." ] }, { "cell_type": "code", "execution_count": 13, "metadata": { "nbgrader": { "grade": true, "grade_id": "cell-cec829da5f2ee5f9", "locked": false, "points": 0, "schema_version": 3, "solution": true } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Sequence:\n", "DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYTTPPTFGQGTKVEIKREVQLVESGGGLVQPGGSLRLSCAASGFTISNSGIHWVRQAPGKGLEWVGWIYPTGGATDYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFWWRSFDYWGQGTLVTVSSIIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISWGDGCGRLHKPGVYTRVANYVDWINDRIR\n", "\n", "Sequence:\n", "DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYTTPPTFGQGTKVEIKREVQLVESGGGLVQPGGSLRLSCAASGFTISNSGIHWVRQAPGKGLEWVGWIYPTGGATDYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFWWRSFDYWGQGTLVTVSSIIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISWGDGCGRLHKPGVYTRVANYVDWINDRIR\n" ] } ], "source": [ "### BEGIN SOLUTION\n", "\n", "seq_metric = metrics.SequenceMetric()\n", "\n", "print(\"Sequence:\")\n", "print(seq_metric.calculate(pose))\n", "\n", "\n", "#OR\n", "print(\"\\nSequence:\")\n", "print(pose.sequence())\n", "\n", "### END SOLUTION" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Regional Packing\n", "\n", "Lets pack just a single CDR loop. How do we do this? Use a `TaskFactory` and a `TaskOperation`. \n", " To make things easier, we will use a `ResidueSelector` to select the CDR. You will see more of this later.\n", " Briefly, a ResidueSelector returns a boolean vector that is the length of the pose. Each boolean is an indication of whether the residue was selected or not. Because the vector is the same length of the pose, the index is the residue number. There are many `ResidueSelectors` in rosetta, including ones for `AND` and `OR` operations to combine them. Note where most of them come from above: `from rosetta.core.select import residue_selector as selections`\n", "\n", "### Make selection using the CDRResidueSelector and NeighborhoodResidueSelector\n", "\n", "We will use the NeighborhoodResidueSelector to pack the CDR loop and its surrounding neighbors, which defaults to 6 angstrums. Each time we pack, the TaskFactory will be used to generate packing instructions (`PackerTask`) - and subsequently, the neighbors that we are packing will be updated each time to reflect this changing state of the pose." ] }, { "cell_type": "code", "execution_count": 32, "metadata": {}, "outputs": [], "source": [ "nbr_selector = selections.NeighborhoodResidueSelector()\n", "cdr_selector = CDRResidueSelector()\n", "cdr_selector.set_cdr(h1)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Note that h1 is what is called an enum. It is a named integer. This is better than passing around strings, \n", " and you will start to see many of these around Rosetta. They were imported when we imported the antibody namespace at \n", " the top of this workshop. Score terms such as fa_dun are also enums." ] }, { "cell_type": "code", "execution_count": 33, "metadata": {}, "outputs": [], "source": [ "nbr_selector.set_focus_selector(cdr_selector)\n", "nbr_selector.set_include_focus_in_subset(True)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Restrict to our selection\n", "\n", "Lets turn off packing for everything but the H1 loop and its neighbors. By using a TF, every time packing is done,\n", " we regenerate the neighbors. Using the NeighborhoodResidueSelector we actually use the pose energies object that\n", " has a list of neighbors instead of doing an N by N calculation each time!\n", " \n", "In order to do this, we create what is known as a Residue Level Task Operation, or RLT, and then pass that into the `OperateOnResidueSubset`. Use your tab completion to see how many RLTs there are." ] }, { "cell_type": "code", "execution_count": 34, "metadata": {}, "outputs": [], "source": [ "prevent_repacking_rlt = operation.PreventRepackingRLT()" ] }, { "cell_type": "code", "execution_count": 35, "metadata": {}, "outputs": [], "source": [ "#True indicates here that we are flipping the selection. So that we are turning off everything but the CDR and\n", "# its neighbors.\n", "\n", "prevent_subset_repacking = operation.OperateOnResidueSubset(prevent_repacking_rlt, nbr_selector, True )\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Lets check to see what residues have been selected as the CDR, and then the CDR and its neighbors. We will use this to make sure our PackerTask is setup properly" ] }, { "cell_type": "code", "execution_count": 36, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "CDR\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "131\n", "132\n", "133\n", "134\n", "135\n", "136\n", "137\n", "138\n", "139\n", "140\n", "141\n", "142\n", "143\n", "\n", "CDR+Neighbors\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "96\n", "109\n", "110\n", "111\n", "112\n", "113\n", "114\n", "115\n", "129\n", "130\n", "131 CDR\n", "132 CDR\n", "133 CDR\n", "134 CDR\n", "135 CDR\n", "136 CDR\n", "137 CDR\n", "138 CDR\n", "139 CDR\n", "140 CDR\n", "141 CDR\n", "142 CDR\n", "143 CDR\n", "144\n", "145\n", "155\n", "156\n", "157\n", "158\n", "159\n", "160\n", "161\n", "162\n", "163\n", "165\n", "167\n", "178\n", "180\n", "181\n", "182\n", "183\n", "184\n", "185\n", "186\n", "187\n", "203\n", "204\n", "205\n", "206\n", "207\n", "208\n", "212\n", "214\n", "215\n", "216\n", "268\n", "269\n", "270\n", "302\n", "304\n", "305\n", "306\n", "307\n", "308\n", "309\n" ] } ], "source": [ "cdr_res = []\n", "print(\"CDR\")\n", "for i in select.get_residue_set_from_subset(cdr_selector.apply(pose)):\n", " print(i)\n", " cdr_res.append(i)\n", " \n", "print(\"\\nCDR+Neighbors\")\n", "for i in select.get_residue_set_from_subset(nbr_selector.apply(pose)):\n", " if i in cdr_res:\n", " print(i,\"CDR\")\n", " else:\n", " print(i)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Reset the pose" ] }, { "cell_type": "code", "execution_count": 37, "metadata": {}, "outputs": [], "source": [ "\n", "pose = original_pose.clone()\n", "\n", "tf.push_back(prevent_subset_repacking)\n", "\n", "pack_cdrs_and_neighbors_tf = tf.clone()\n", "\n", "packer.task_factory(tf)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Before we start, lets take a look at our PackerTask. Are we designing anything? Does this match our selection?" ] }, { "cell_type": "code", "execution_count": 38, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "#Packer_Task\n", "\n", "resid\tpack?\tdesign?\tallowed_aas\n", "1\tFALSE\tFALSE\t\n", "2\tFALSE\tFALSE\t\n", "3\tFALSE\tFALSE\t\n", "4\tFALSE\tFALSE\t\n", "5\tFALSE\tFALSE\t\n", "6\tFALSE\tFALSE\t\n", "7\tFALSE\tFALSE\t\n", "8\tFALSE\tFALSE\t\n", "9\tFALSE\tFALSE\t\n", "10\tFALSE\tFALSE\t\n", "11\tFALSE\tFALSE\t\n", "12\tFALSE\tFALSE\t\n", "13\tFALSE\tFALSE\t\n", "14\tFALSE\tFALSE\t\n", "15\tFALSE\tFALSE\t\n", "16\tFALSE\tFALSE\t\n", "17\tFALSE\tFALSE\t\n", "18\tFALSE\tFALSE\t\n", "19\tFALSE\tFALSE\t\n", "20\tFALSE\tFALSE\t\n", "21\tFALSE\tFALSE\t\n", "22\tFALSE\tFALSE\t\n", "23\tFALSE\tFALSE\t\n", "24\tFALSE\tFALSE\t\n", "25\tFALSE\tFALSE\t\n", "26\tFALSE\tFALSE\t\n", "27\tFALSE\tFALSE\t\n", "28\tFALSE\tFALSE\t\n", "29\tFALSE\tFALSE\t\n", "30\tFALSE\tFALSE\t\n", "31\tFALSE\tFALSE\t\n", "32\tFALSE\tFALSE\t\n", "33\tFALSE\tFALSE\t\n", "34\tFALSE\tFALSE\t\n", "35\tFALSE\tFALSE\t\n", "36\tFALSE\tFALSE\t\n", "37\tFALSE\tFALSE\t\n", "38\tFALSE\tFALSE\t\n", "39\tFALSE\tFALSE\t\n", "40\tFALSE\tFALSE\t\n", "41\tFALSE\tFALSE\t\n", "42\tFALSE\tFALSE\t\n", "43\tFALSE\tFALSE\t\n", "44\tFALSE\tFALSE\t\n", "45\tFALSE\tFALSE\t\n", "46\tFALSE\tFALSE\t\n", "47\tFALSE\tFALSE\t\n", "48\tFALSE\tFALSE\t\n", "49\tFALSE\tFALSE\t\n", "50\tFALSE\tFALSE\t\n", "51\tFALSE\tFALSE\t\n", "52\tFALSE\tFALSE\t\n", "53\tFALSE\tFALSE\t\n", "54\tFALSE\tFALSE\t\n", "55\tFALSE\tFALSE\t\n", "56\tFALSE\tFALSE\t\n", "57\tFALSE\tFALSE\t\n", "58\tFALSE\tFALSE\t\n", "59\tFALSE\tFALSE\t\n", "60\tFALSE\tFALSE\t\n", "61\tFALSE\tFALSE\t\n", "62\tFALSE\tFALSE\t\n", "63\tFALSE\tFALSE\t\n", "64\tFALSE\tFALSE\t\n", "65\tFALSE\tFALSE\t\n", "66\tFALSE\tFALSE\t\n", "67\tFALSE\tFALSE\t\n", "68\tFALSE\tFALSE\t\n", "69\tFALSE\tFALSE\t\n", "70\tFALSE\tFALSE\t\n", "71\tFALSE\tFALSE\t\n", "72\tFALSE\tFALSE\t\n", "73\tFALSE\tFALSE\t\n", "74\tFALSE\tFALSE\t\n", "75\tFALSE\tFALSE\t\n", "76\tFALSE\tFALSE\t\n", "77\tFALSE\tFALSE\t\n", "78\tFALSE\tFALSE\t\n", "79\tFALSE\tFALSE\t\n", "80\tFALSE\tFALSE\t\n", "81\tFALSE\tFALSE\t\n", "82\tFALSE\tFALSE\t\n", "83\tFALSE\tFALSE\t\n", "84\tFALSE\tFALSE\t\n", "85\tFALSE\tFALSE\t\n", "86\tFALSE\tFALSE\t\n", "87\tFALSE\tFALSE\t\n", "88\tFALSE\tFALSE\t\n", "89\tFALSE\tFALSE\t\n", "90\tFALSE\tFALSE\t\n", "91\tFALSE\tFALSE\t\n", "92\tFALSE\tFALSE\t\n", "93\tFALSE\tFALSE\t\n", "94\tFALSE\tFALSE\t\n", "95\tFALSE\tFALSE\t\n", "96\tTRUE\tFALSE\tPRO\n", "97\tFALSE\tFALSE\t\n", "98\tFALSE\tFALSE\t\n", "99\tFALSE\tFALSE\t\n", "100\tFALSE\tFALSE\t\n", "101\tFALSE\tFALSE\t\n", "102\tFALSE\tFALSE\t\n", "103\tFALSE\tFALSE\t\n", "104\tFALSE\tFALSE\t\n", "105\tFALSE\tFALSE\t\n", "106\tFALSE\tFALSE\t\n", "107\tFALSE\tFALSE\t\n", "108\tFALSE\tFALSE\t\n", "109\tTRUE\tFALSE\tGLU:NtermProteinFull\n", "110\tTRUE\tFALSE\tVAL\n", "111\tTRUE\tFALSE\tGLN\n", "112\tTRUE\tFALSE\tLEU\n", "113\tTRUE\tFALSE\tVAL\n", "114\tTRUE\tFALSE\tGLU\n", "115\tTRUE\tFALSE\tSER\n", "116\tFALSE\tFALSE\t\n", "117\tFALSE\tFALSE\t\n", "118\tFALSE\tFALSE\t\n", "119\tFALSE\tFALSE\t\n", "120\tFALSE\tFALSE\t\n", "121\tFALSE\tFALSE\t\n", "122\tFALSE\tFALSE\t\n", "123\tFALSE\tFALSE\t\n", "124\tFALSE\tFALSE\t\n", "125\tFALSE\tFALSE\t\n", "126\tFALSE\tFALSE\t\n", "127\tFALSE\tFALSE\t\n", "128\tFALSE\tFALSE\t\n", "129\tTRUE\tFALSE\tSER\n", "130\tTRUE\tFALSE\tCYS:disulfide\n", "131\tFALSE\tFALSE\t\n", "132\tFALSE\tFALSE\t\n", "133\tFALSE\tFALSE\t\n", "134\tFALSE\tFALSE\t\n", "135\tFALSE\tFALSE\t\n", "136\tFALSE\tFALSE\t\n", "137\tFALSE\tFALSE\t\n", "138\tFALSE\tFALSE\t\n", "139\tFALSE\tFALSE\t\n", "140\tFALSE\tFALSE\t\n", "141\tFALSE\tFALSE\t\n", "142\tFALSE\tFALSE\t\n", "143\tFALSE\tFALSE\t\n", "144\tTRUE\tFALSE\tTRP\n", "145\tTRUE\tFALSE\tVAL\n", "146\tFALSE\tFALSE\t\n", "147\tFALSE\tFALSE\t\n", "148\tFALSE\tFALSE\t\n", "149\tFALSE\tFALSE\t\n", "150\tFALSE\tFALSE\t\n", "151\tFALSE\tFALSE\t\n", "152\tFALSE\tFALSE\t\n", "153\tFALSE\tFALSE\t\n", "154\tFALSE\tFALSE\t\n", "155\tTRUE\tFALSE\tTRP\n", "156\tTRUE\tFALSE\tVAL\n", "157\tTRUE\tFALSE\tGLY\n", "158\tTRUE\tFALSE\tTRP\n", "159\tTRUE\tFALSE\tILE\n", "160\tTRUE\tFALSE\tTYR\n", "161\tTRUE\tFALSE\tPRO\n", "162\tTRUE\tFALSE\tTHR\n", "163\tTRUE\tFALSE\tGLY\n", "164\tFALSE\tFALSE\t\n", "165\tTRUE\tFALSE\tALA\n", "166\tFALSE\tFALSE\t\n", "167\tTRUE\tFALSE\tASP\n", "168\tFALSE\tFALSE\t\n", "169\tFALSE\tFALSE\t\n", "170\tFALSE\tFALSE\t\n", "171\tFALSE\tFALSE\t\n", "172\tFALSE\tFALSE\t\n", "173\tFALSE\tFALSE\t\n", "174\tFALSE\tFALSE\t\n", "175\tFALSE\tFALSE\t\n", "176\tFALSE\tFALSE\t\n", "177\tFALSE\tFALSE\t\n", "178\tTRUE\tFALSE\tILE\n", "179\tFALSE\tFALSE\t\n", "180\tTRUE\tFALSE\tALA\n", "181\tTRUE\tFALSE\tASP\n", "182\tTRUE\tFALSE\tTHR\n", "183\tTRUE\tFALSE\tSER\n", "184\tTRUE\tFALSE\tLYS\n", "185\tTRUE\tFALSE\tASN\n", "186\tTRUE\tFALSE\tTHR\n", "187\tTRUE\tFALSE\tALA\n", "188\tFALSE\tFALSE\t\n", "189\tFALSE\tFALSE\t\n", "190\tFALSE\tFALSE\t\n", "191\tFALSE\tFALSE\t\n", "192\tFALSE\tFALSE\t\n", "193\tFALSE\tFALSE\t\n", "194\tFALSE\tFALSE\t\n", "195\tFALSE\tFALSE\t\n", "196\tFALSE\tFALSE\t\n", "197\tFALSE\tFALSE\t\n", "198\tFALSE\tFALSE\t\n", "199\tFALSE\tFALSE\t\n", "200\tFALSE\tFALSE\t\n", "201\tFALSE\tFALSE\t\n", "202\tFALSE\tFALSE\t\n", "203\tTRUE\tFALSE\tTYR\n", "204\tTRUE\tFALSE\tCYS:disulfide\n", "205\tTRUE\tFALSE\tALA\n", "206\tTRUE\tFALSE\tARG\n", "207\tTRUE\tFALSE\tPHE\n", "208\tTRUE\tFALSE\tTRP\n", "209\tFALSE\tFALSE\t\n", "210\tFALSE\tFALSE\t\n", "211\tFALSE\tFALSE\t\n", "212\tTRUE\tFALSE\tPHE\n", "213\tFALSE\tFALSE\t\n", "214\tTRUE\tFALSE\tTYR\n", "215\tTRUE\tFALSE\tTRP\n", "216\tTRUE\tFALSE\tGLY\n", "217\tFALSE\tFALSE\t\n", "218\tFALSE\tFALSE\t\n", "219\tFALSE\tFALSE\t\n", "220\tFALSE\tFALSE\t\n", "221\tFALSE\tFALSE\t\n", "222\tFALSE\tFALSE\t\n", "223\tFALSE\tFALSE\t\n", "224\tFALSE\tFALSE\t\n", "225\tFALSE\tFALSE\t\n", "226\tFALSE\tFALSE\t\n", "227\tFALSE\tFALSE\t\n", "228\tFALSE\tFALSE\t\n", "229\tFALSE\tFALSE\t\n", "230\tFALSE\tFALSE\t\n", "231\tFALSE\tFALSE\t\n", "232\tFALSE\tFALSE\t\n", "233\tFALSE\tFALSE\t\n", "234\tFALSE\tFALSE\t\n", "235\tFALSE\tFALSE\t\n", "236\tFALSE\tFALSE\t\n", "237\tFALSE\tFALSE\t\n", "238\tFALSE\tFALSE\t\n", "239\tFALSE\tFALSE\t\n", "240\tFALSE\tFALSE\t\n", "241\tFALSE\tFALSE\t\n", "242\tFALSE\tFALSE\t\n", "243\tFALSE\tFALSE\t\n", "244\tFALSE\tFALSE\t\n", "245\tFALSE\tFALSE\t\n", "246\tFALSE\tFALSE\t\n", "247\tFALSE\tFALSE\t\n", "248\tFALSE\tFALSE\t\n", "249\tFALSE\tFALSE\t\n", "250\tFALSE\tFALSE\t\n", "251\tFALSE\tFALSE\t\n", "252\tFALSE\tFALSE\t\n", "253\tFALSE\tFALSE\t\n", "254\tFALSE\tFALSE\t\n", "255\tFALSE\tFALSE\t\n", "256\tFALSE\tFALSE\t\n", "257\tFALSE\tFALSE\t\n", "258\tFALSE\tFALSE\t\n", "259\tFALSE\tFALSE\t\n", "260\tFALSE\tFALSE\t\n", "261\tFALSE\tFALSE\t\n", "262\tFALSE\tFALSE\t\n", "263\tFALSE\tFALSE\t\n", "264\tFALSE\tFALSE\t\n", "265\tFALSE\tFALSE\t\n", "266\tFALSE\tFALSE\t\n", "267\tFALSE\tFALSE\t\n", "268\tTRUE\tFALSE\tSER\n", "269\tTRUE\tFALSE\tHIS,HIS_D\n", "270\tTRUE\tFALSE\tSER\n", "271\tFALSE\tFALSE\t\n", "272\tFALSE\tFALSE\t\n", "273\tFALSE\tFALSE\t\n", "274\tFALSE\tFALSE\t\n", "275\tFALSE\tFALSE\t\n", "276\tFALSE\tFALSE\t\n", "277\tFALSE\tFALSE\t\n", "278\tFALSE\tFALSE\t\n", "279\tFALSE\tFALSE\t\n", "280\tFALSE\tFALSE\t\n", "281\tFALSE\tFALSE\t\n", "282\tFALSE\tFALSE\t\n", "283\tFALSE\tFALSE\t\n", "284\tFALSE\tFALSE\t\n", "285\tFALSE\tFALSE\t\n", "286\tFALSE\tFALSE\t\n", "287\tFALSE\tFALSE\t\n", "288\tFALSE\tFALSE\t\n", "289\tFALSE\tFALSE\t\n", "290\tFALSE\tFALSE\t\n", "291\tFALSE\tFALSE\t\n", "292\tFALSE\tFALSE\t\n", "293\tFALSE\tFALSE\t\n", "294\tFALSE\tFALSE\t\n", "295\tFALSE\tFALSE\t\n", "296\tFALSE\tFALSE\t\n", "297\tFALSE\tFALSE\t\n", "298\tFALSE\tFALSE\t\n", "299\tFALSE\tFALSE\t\n", "300\tFALSE\tFALSE\t\n", "301\tFALSE\tFALSE\t\n", "302\tTRUE\tFALSE\tPRO\n", "303\tFALSE\tFALSE\t\n", "304\tTRUE\tFALSE\tTHR\n", "305\tTRUE\tFALSE\tLEU\n", "306\tTRUE\tFALSE\tTYR\n", "307\tTRUE\tFALSE\tSER\n", "308\tTRUE\tFALSE\tVAL\n", "309\tTRUE\tFALSE\tPHE\n", "310\tFALSE\tFALSE\t\n", "311\tFALSE\tFALSE\t\n", "312\tFALSE\tFALSE\t\n", "313\tFALSE\tFALSE\t\n", "314\tFALSE\tFALSE\t\n", "315\tFALSE\tFALSE\t\n", "316\tFALSE\tFALSE\t\n", "317\tFALSE\tFALSE\t\n", "318\tFALSE\tFALSE\t\n", "319\tFALSE\tFALSE\t\n", "320\tFALSE\tFALSE\t\n", "321\tFALSE\tFALSE\t\n", "322\tFALSE\tFALSE\t\n", "323\tFALSE\tFALSE\t\n", "324\tFALSE\tFALSE\t\n", "325\tFALSE\tFALSE\t\n", "326\tFALSE\tFALSE\t\n", "327\tFALSE\tFALSE\t\n", "328\tFALSE\tFALSE\t\n", "329\tFALSE\tFALSE\t\n", "330\tFALSE\tFALSE\t\n", "331\tFALSE\tFALSE\t\n", "332\tFALSE\tFALSE\t\n", "333\tFALSE\tFALSE\t\n", "334\tFALSE\tFALSE\t\n", "335\tFALSE\tFALSE\t\n", "336\tFALSE\tFALSE\t\n", "337\tFALSE\tFALSE\t\n", "338\tFALSE\tFALSE\t\n", "339\tFALSE\tFALSE\t\n", "340\tFALSE\tFALSE\t\n", "341\tFALSE\tFALSE\t\n", "342\tFALSE\tFALSE\t\n", "343\tFALSE\tFALSE\t\n", "344\tFALSE\tFALSE\t\n", "345\tFALSE\tFALSE\t\n", "346\tFALSE\tFALSE\t\n", "347\tFALSE\tFALSE\t\n", "348\tFALSE\tFALSE\t\n", "349\tFALSE\tFALSE\t\n", "350\tFALSE\tFALSE\t\n", "351\tFALSE\tFALSE\t\n", "352\tFALSE\tFALSE\t\n", "353\tFALSE\tFALSE\t\n", "354\tFALSE\tFALSE\t\n", "355\tFALSE\tFALSE\t\n", "356\tFALSE\tFALSE\t\n", "357\tFALSE\tFALSE\t\n", "358\tFALSE\tFALSE\t\n", "359\tFALSE\tFALSE\t\n", "360\tFALSE\tFALSE\t\n", "361\tFALSE\tFALSE\t\n", "362\tFALSE\tFALSE\t\n", "363\tFALSE\tFALSE\t\n", "364\tFALSE\tFALSE\t\n", "365\tFALSE\tFALSE\t\n", "366\tFALSE\tFALSE\t\n", "367\tFALSE\tFALSE\t\n", "368\tFALSE\tFALSE\t\n", "369\tFALSE\tFALSE\t\n", "370\tFALSE\tFALSE\t\n", "371\tFALSE\tFALSE\t\n", "372\tFALSE\tFALSE\t\n", "373\tFALSE\tFALSE\t\n", "374\tFALSE\tFALSE\t\n", "375\tFALSE\tFALSE\t\n", "376\tFALSE\tFALSE\t\n", "377\tFALSE\tFALSE\t\n", "378\tFALSE\tFALSE\t\n", "379\tFALSE\tFALSE\t\n", "380\tFALSE\tFALSE\t\n", "381\tFALSE\tFALSE\t\n", "382\tFALSE\tFALSE\t\n", "383\tFALSE\tFALSE\t\n", "384\tFALSE\tFALSE\t\n", "385\tFALSE\tFALSE\t\n", "386\tFALSE\tFALSE\t\n", "387\tFALSE\tFALSE\t\n", "388\tFALSE\tFALSE\t\n", "389\tFALSE\tFALSE\t\n", "390\tFALSE\tFALSE\t\n", "391\tFALSE\tFALSE\t\n", "392\tFALSE\tFALSE\t\n", "393\tFALSE\tFALSE\t\n", "394\tFALSE\tFALSE\t\n", "395\tFALSE\tFALSE\t\n", "396\tFALSE\tFALSE\t\n", "397\tFALSE\tFALSE\t\n", "398\tFALSE\tFALSE\t\n", "399\tFALSE\tFALSE\t\n", "400\tFALSE\tFALSE\t\n", "401\tFALSE\tFALSE\t\n", "402\tFALSE\tFALSE\t\n", "403\tFALSE\tFALSE\t\n", "404\tFALSE\tFALSE\t\n", "405\tFALSE\tFALSE\t\n", "406\tFALSE\tFALSE\t\n", "407\tFALSE\tFALSE\t\n", "408\tFALSE\tFALSE\t\n", "409\tFALSE\tFALSE\t\n", "410\tFALSE\tFALSE\t\n", "411\tFALSE\tFALSE\t\n", "412\tFALSE\tFALSE\t\n", "413\tFALSE\tFALSE\t\n", "414\tFALSE\tFALSE\t\n", "415\tFALSE\tFALSE\t\n", "416\tFALSE\tFALSE\t\n", "417\tFALSE\tFALSE\t\n", "418\tFALSE\tFALSE\t\n", "419\tFALSE\tFALSE\t\n", "420\tFALSE\tFALSE\t\n", "421\tFALSE\tFALSE\t\n", "422\tFALSE\tFALSE\t\n", "423\tFALSE\tFALSE\t\n", "424\tFALSE\tFALSE\t\n", "425\tFALSE\tFALSE\t\n", "426\tFALSE\tFALSE\t\n", "427\tFALSE\tFALSE\t\n", "428\tFALSE\tFALSE\t\n", "429\tFALSE\tFALSE\t\n", "430\tFALSE\tFALSE\t\n", "431\tFALSE\tFALSE\t\n", "432\tFALSE\tFALSE\t\n", "433\tFALSE\tFALSE\t\n", "434\tFALSE\tFALSE\t\n", "435\tFALSE\tFALSE\t\n", "436\tFALSE\tFALSE\t\n", "437\tFALSE\tFALSE\t\n", "438\tFALSE\tFALSE\t\n", "439\tFALSE\tFALSE\t\n", "440\tFALSE\tFALSE\t\n", "441\tFALSE\tFALSE\t\n", "442\tFALSE\tFALSE\t\n", "443\tFALSE\tFALSE\t\n", "444\tFALSE\tFALSE\t\n", "445\tFALSE\tFALSE\t\n", "446\tFALSE\tFALSE\t\n", "447\tFALSE\tFALSE\t\n", "448\tFALSE\tFALSE\t\n", "449\tFALSE\tFALSE\t\n", "450\tFALSE\tFALSE\t\n", "451\tFALSE\tFALSE\t\n", "452\tFALSE\tFALSE\t\n", "453\tFALSE\tFALSE\t\n", "454\tFALSE\tFALSE\t\n", "455\tFALSE\tFALSE\t\n", "456\tFALSE\tFALSE\t\n", "457\tFALSE\tFALSE\t\n", "458\tFALSE\tFALSE\t\n", "459\tFALSE\tFALSE\t\n", "460\tFALSE\tFALSE\t\n", "461\tFALSE\tFALSE\t\n", "462\tFALSE\tFALSE\t\n", "463\tFALSE\tFALSE\t\n", "464\tFALSE\tFALSE\t\n", "\n" ] } ], "source": [ "print(tf.create_task_and_apply_taskoperations(pose))" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Now lets Run the packer and dump the PDB.\n", "\n", "Note how many rotamers were used and how many positions were done. Now run it again. Have those numbers changed?\n", " Why?" ] }, { "cell_type": "code", "execution_count": 39, "metadata": { "nbgrader": { "grade": true, "grade_id": "cell-08b16c378d66130f", "locked": false, "points": 0, "schema_version": 3, "solution": true } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 1952 rotamers at 52 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n" ] }, { "data": { "text/plain": [ "True" ] }, "execution_count": 39, "metadata": {}, "output_type": "execute_result" } ], "source": [ "### BEGIN SOLUTION\n", "\n", "#Skip for tests\n", "if not os.getenv(\"DEBUG\"):\n", " packer.apply(pose)\n", " \n", "pose.dump_pdb(\"outputs/2r0l_cdr_repack.pdb\")\n", "\n", "### END SOLUTION" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Design\n", "\n", "Lets design this CDR. We already almost everything we need created, so lets do this!!\n", "\n", "Note, since we added the RestrictToRepacking TaskOperation to our original `TaskFactory`, we need to reset (clear) it. " ] }, { "cell_type": "code", "execution_count": 40, "metadata": {}, "outputs": [], "source": [ "\n", "pose = original_pose.clone()\n", "\n", "tf.clear()\n", "tf.push_back(operation.InitializeFromCommandline())\n", "tf.push_back(prevent_subset_repacking)\n", "\n", "#Turn off design of neighbors\n", "nbr_selector2 = selections.NeighborhoodResidueSelector()\n", "nbr_selector2.set_focus_selector(cdr_selector)\n", "nbr_selector2.set_include_focus_in_subset(False)\n", "\n", "restrict_to_repack = operation.RestrictToRepackingRLT()\n", "prevent_nbr_design = operation.OperateOnResidueSubset(restrict_to_repack, nbr_selector2, False )\n", "tf.push_back(prevent_nbr_design)\n", "\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Once again, lets check to make sure we have created the correct TaskFactory. You should now see that the CDRs we selected are set to design into any of the amino acids. " ] }, { "cell_type": "code", "execution_count": 41, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "#Packer_Task\n", "\n", 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"426\tFALSE\tFALSE\t\n", "427\tFALSE\tFALSE\t\n", "428\tFALSE\tFALSE\t\n", "429\tFALSE\tFALSE\t\n", "430\tFALSE\tFALSE\t\n", "431\tFALSE\tFALSE\t\n", "432\tFALSE\tFALSE\t\n", "433\tFALSE\tFALSE\t\n", "434\tFALSE\tFALSE\t\n", "435\tFALSE\tFALSE\t\n", "436\tFALSE\tFALSE\t\n", "437\tFALSE\tFALSE\t\n", "438\tFALSE\tFALSE\t\n", "439\tFALSE\tFALSE\t\n", "440\tFALSE\tFALSE\t\n", "441\tFALSE\tFALSE\t\n", "442\tFALSE\tFALSE\t\n", "443\tFALSE\tFALSE\t\n", "444\tFALSE\tFALSE\t\n", "445\tFALSE\tFALSE\t\n", "446\tFALSE\tFALSE\t\n", "447\tFALSE\tFALSE\t\n", "448\tFALSE\tFALSE\t\n", "449\tFALSE\tFALSE\t\n", "450\tFALSE\tFALSE\t\n", "451\tFALSE\tFALSE\t\n", "452\tFALSE\tFALSE\t\n", "453\tFALSE\tFALSE\t\n", "454\tFALSE\tFALSE\t\n", "455\tFALSE\tFALSE\t\n", "456\tFALSE\tFALSE\t\n", "457\tFALSE\tFALSE\t\n", "458\tFALSE\tFALSE\t\n", "459\tFALSE\tFALSE\t\n", "460\tFALSE\tFALSE\t\n", "461\tFALSE\tFALSE\t\n", "462\tFALSE\tFALSE\t\n", "463\tFALSE\tFALSE\t\n", "464\tFALSE\tFALSE\t\n", "\n" ] } ], "source": [ "print(tf.create_task_and_apply_taskoperations(pose))" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Set and Run\n", "\n", "Set the new tf to the packer and run it. This will take a few minutes as for each CDR we packing rotamers for all 20 amino acids instead of just the native residue. Take note of how many rotamers are built compared to when we didn't do any design.\n", "\n", "Dump the PDB and take a look. " ] }, { "cell_type": "code", "execution_count": 42, "metadata": { "nbgrader": { "grade": true, "grade_id": "cell-b968c1e06844bc48", "locked": false, "points": 0, "schema_version": 3, "solution": true } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 15803 rotamers at 65 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating PDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n" ] }, { "data": { "text/plain": [ "True" ] }, "execution_count": 42, "metadata": {}, "output_type": "execute_result" } ], "source": [ "### BEGIN SOLUTION\n", "\n", "packer.task_factory(tf)\n", "\n", "#Skip for tests\n", "if not os.getenv(\"DEBUG\"):\n", " packer.apply(pose)\n", " \n", "pose.dump_pdb(\"outputs/2r0l_cdr_design.pdb\")\n", "\n", "### END SOLUTION" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Relax\n", "\n", "Lets first relax the whole protein. This will take some time, so after you run it, take a break and stretch! As usual, you can find the output in the `expected_outputs` directory of this directory.\n" ] }, { "cell_type": "code", "execution_count": 55, "metadata": {}, "outputs": [], "source": [ "\n", "pose = original_pose.clone()\n", "fr = FastRelax()\n", "\n", "#Here, we have to set a scorefunction or we segfault. \n", "# Error checking is important, and protocols should use a default scorefunction. We will manage.\n", "\n", "fr.set_scorefxn(scorefxn)\n", "\n", "#Lets run this. This takes a very long time, so we are going decrease the amount of minimization cycles we use.\n", "# This is generally only recommended for cartesian, but we just want everything to run fast at the moment.\n", "fr.max_iter(100)\n", "\n", "#Run the code\n", "\n", "#Dump the pdb and take a look." ] }, { "cell_type": "code", "execution_count": 44, "metadata": { "nbgrader": { "grade": true, "grade_id": "cell-f24a49a10fcb07cf", "locked": false, "points": 0, "schema_version": 3, "solution": true } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: repeat -520.742 0 0 0.55\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 23112 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -2274.11 2.36629 2.36629 0.011\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 22197 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -1775.66 1.29813 1.29813 0.1375\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 20679 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -1636.07 0.885842 0.885842 0.3025\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 18762 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -1474.81 0.74887 0.74887 0.55\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mMRP: 0 -1474.81 -1474.81 0.74887 0.74887\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: accept_to_best -1474.81 0.74887 0.74887 0.55\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: endrepeat -1474.81 0.74887 0.74887 0.55\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 22507 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -2379.43 2.67173 2.67173 0.011\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 22466 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -1819.36 1.38682 1.38682 0.1375\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 20203 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -1647.92 1.06563 1.06563 0.3025\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 18909 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -1479.55 0.872626 0.872626 0.55\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mMRP: 1 -1479.55 -1479.55 0.872626 0.872626\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: accept_to_best -1479.55 0.872626 0.872626 0.55\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: endrepeat -1479.55 0.872626 0.872626 0.55\n", "\u001b[0mprotocols::checkpoint: \u001b[0mDeleting checkpoints of FastRelax\n" ] }, { "data": { "text/plain": [ "True" ] }, "execution_count": 44, "metadata": {}, "output_type": "execute_result" } ], "source": [ "### BEGIN SOLUTION\n", "#Skip for tests\n", "if not os.getenv(\"DEBUG\"):\n", " fr.apply(pose)\n", " \n", "pose.dump_pdb(\"outputs/2r0l_relaxed.pdb\")\n", "\n", "### END SOLUTION" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Check the energy difference here once again. Note how low it is compared to simply packing\n", "\n", "delta = ?" ] }, { "cell_type": "code", "execution_count": 50, "metadata": { "nbgrader": { "grade": true, "grade_id": "cell-6ba91002ffac69a7", "locked": false, "points": 0, "schema_version": 3, "solution": true } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "relaxed -1479.54882708\n", "original -520.742210502\n", "delta -958.806616578\n" ] } ], "source": [ "### BEGIN SOLUTION\n", "print(\"relaxed \",scorefxn(pose))\n", "print(\"original\",scorefxn(original_pose))\n", "delta = scorefxn(pose) - scorefxn(original_pose)\n", "print(\"delta \",delta)\n", "### END SOLUTION" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Regional Relax\n", "\n", "So that was fun, but what we really want is to optimize regions of the protein that we care about. \n", " This can be tricky, so to start off, lets do the basic thing and see what happens. \n", " \n", "We will use a `MoveMapFactory`, which allows us to use `ResidueSelectors`. \n", "More information on the `MoveMapFactory` in terms of RosettaScripts, can be found here: https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/MoveMapFactories/MoveMapFactories-RosettaScripts\n", "\n", "The default is to have everything OFF first, and turn specific things on." ] }, { "cell_type": "code", "execution_count": 52, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n" ] } ], "source": [ "\n", "pose = original_pose.clone()\n", "mmf = MoveMapFactory()\n", "\n", "#mm_enable and mm_disable are Enums (numbered variables) that come when we import the MMF\n", "mmf.add_bb_action(mm_enable, cdr_selector)\n", "#mmf.add_chi_action(mm_enable, cdr_selector) We are taking this out for speed.\n", "\n", "mm = mmf.create_movemap_from_pose(pose)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Lets take a look at our `MoveMap` that the `MoveMapFactory` creates. Pass the movemap to `print()` We should only have a few residues there.\n", "\n", "Here, we only want to pack the region and neighbors. NOT all 500 residues!\n", "\n", "Lets use the cloned TaskFactory we used to repack the CDRs and neighbors, since we will be allowing the backbone of the CDRs to move." ] }, { "cell_type": "code", "execution_count": 53, "metadata": {}, "outputs": [], "source": [ "fr.set_movemap_factory(mmf)\n", "fr.set_task_factory(pack_cdrs_and_neighbors_tf)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Run this, take a break and then lets see the results.\n", "Dump the pose and take a look at it. " ] }, { "cell_type": "code", "execution_count": 54, "metadata": { "nbgrader": { "grade": true, "grade_id": "cell-897997d6124746e0", "locked": false, "points": 0, "schema_version": 3, "solution": true } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: repeat -520.742 0 0 0.55\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC 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Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mbasic.io.database: 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DensePDInteractionGraph\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 20 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -1107.12 1.3573 1.3573 0.011\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 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TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 2235 rotamers at 62 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 20 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -737.418 0.80441 0.80441 0.1375\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 2103 rotamers at 57 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 20 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -765.555 0.342906 0.342906 0.3025\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: 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Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 2030 rotamers at 55 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 20 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -660.025 0.262438 0.262438 0.55\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mMRP: 0 -660.025 -660.025 0.262438 0.262438\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: accept_to_best -660.025 0.262438 0.262438 0.55\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: endrepeat -660.025 0.262438 0.262438 0.55\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: 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definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 3000 rotamers at 54 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 20 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -1161.16 1.43343 1.43343 0.011\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 2284 rotamers at 60 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 20 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -796.449 0.632186 0.632186 0.1375\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 2015 rotamers at 53 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 20 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -747.137 0.590596 0.590596 0.3025\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: 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Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 1926 rotamers at 56 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 20 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -676.771 0.355995 0.355995 0.55\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mMRP: 1 -676.771 -676.771 0.355995 0.355995\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: accept_to_best -676.771 0.355995 0.355995 0.55\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: endrepeat -676.771 0.355995 0.355995 0.55\n", "\u001b[0mprotocols::checkpoint: \u001b[0mDeleting checkpoints of FastRelax\n" ] }, { "data": { "text/plain": [ "True" ] }, "execution_count": 54, "metadata": {}, "output_type": "execute_result" } ], "source": [ "### BEGIN SOLUTION\n", "\n", "#Skip for tests\n", "if not os.getenv(\"DEBUG\"):\n", " fr.apply(pose)\n", " \n", "pose.dump_pdb(\"outputs/2r0l_h1_relaxed.pdb\")\n", "\n", "### END SOLUTION" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "**What is wrong with this Pose???**\n", "\n", "\n", "Okay, so we know whats wrong here, right? Right?\n", "The pose is moving too much where we don't want it. This is due to the FoldTree\n", " There are two fixes for this - modify the foldtree (using a Loop foldtree as you will see in later tutorials) or use cartesian-space refinement. \n", " \n", " Lets do the easier of the two - cartesian!\n", " \n", " ### Regional Relax - Cartesian" ] }, { "cell_type": "code", "execution_count": 56, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0mcore.scoring.CartesianBondedEnergy: \u001b[0mInitializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt\n", "\u001b[0mcore.scoring.CartesianBondedEnergy: \u001b[0mRead 757 bb-independent lengths.\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt\n", "\u001b[0mcore.scoring.CartesianBondedEnergy: \u001b[0mRead 1456 bb-independent angles.\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt\n", "\u001b[0mcore.scoring.CartesianBondedEnergy: \u001b[0mRead 1 bb-independent torsions.\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt\n", "\u001b[0mcore.scoring.CartesianBondedEnergy: \u001b[0mRead 2197 bb-independent improper tors.\n" ] } ], "source": [ "\n", "pose = original_pose.clone()\n", "cart_sf = create_score_function(\"ref2015_cart\")\n", "mmf.set_cartesian(True)\n", "fr.set_movemap_factory(mmf)\n", "fr.set_scorefxn(cart_sf)\n", "fr.cartesian(True)\n", "\n", "#This is a general recommendation for cartesian minimization - it lowers the number of maximum cycles.\n", "# More than this only increases time of protocol, but has little effect on energies/structure\n", "fr.max_iter(200)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Run relax Lets dump the pose and take a look again. Does this look better? How are the energies?" ] }, { "cell_type": "code", "execution_count": 57, "metadata": { "nbgrader": { "grade": true, "grade_id": "cell-f2b1c60beff8a6d8", "locked": false, "points": 0, "schema_version": 3, "solution": true } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mcore.scoring.CartesianBondedEnergy: \u001b[0mCreating new peptide-bonded energy container (464)\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: repeat -230.749 0 0 0.55\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 23112 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 23 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 88 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 130 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 204 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 250 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 258 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 266 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 328 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 353 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 385 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 401 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 412 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 422 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 440 BRANCH 1\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -2393.05 0.88128 0.88128 0.011\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 22793 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 23 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 88 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 130 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 204 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 250 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 258 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 266 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 328 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 353 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 385 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 401 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 412 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 422 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 440 BRANCH 1\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -1944.4 0.721666 0.721666 0.1375\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 20680 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 23 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 88 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 130 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 204 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 250 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 258 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 266 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 328 BRANCH 1\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 353 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 385 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 401 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 412 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 422 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 440 BRANCH 1\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -1782.16 0.65455 0.65455 0.3025\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 19414 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 23 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 88 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 130 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 204 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 250 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 258 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 266 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 328 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 353 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 385 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 401 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 412 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 422 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 440 BRANCH 1\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -1624.65 0.592299 0.592299 0.55\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mMRP: 0 -1624.65 -1624.65 0.592299 0.592299\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: accept_to_best -1624.65 0.592299 0.592299 0.55\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: endrepeat -1624.65 0.592299 0.592299 0.55\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 24179 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 23 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 88 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 130 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 204 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 250 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 258 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 266 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 328 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 353 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 385 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 401 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 412 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 422 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 440 BRANCH 1\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -2526.51 1.19733 1.19733 0.011\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 22124 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 23 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 88 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 130 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 204 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 250 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 258 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 266 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 328 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 353 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 385 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 401 BRANCH 1\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 412 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 422 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 440 BRANCH 1\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -2011.26 0.96739 0.96739 0.1375\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 20397 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 23 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 88 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 130 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 204 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 250 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 258 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 266 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 328 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 353 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 385 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 401 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 412 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 422 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 440 BRANCH 1\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -1820.1 0.848976 0.848976 0.3025\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 19350 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 23 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 88 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 130 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 204 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 250 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 258 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 266 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 328 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 353 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 385 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 401 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 412 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 422 BRANCH 1\n", "\u001b[0mcore.pose.util: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Unable to find atom_tree atom for this Rosetta branch connection angle: residue 440 BRANCH 1\n", "\u001b[0mcore.optimization.Minimizer: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -1652.52 0.756863 0.756863 0.55\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mMRP: 1 -1652.52 -1652.52 0.756863 0.756863\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: accept_to_best -1652.52 0.756863 0.756863 0.55\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: endrepeat -1652.52 0.756863 0.756863 0.55\n", "\u001b[0mprotocols::checkpoint: \u001b[0mDeleting checkpoints of FastRelax\n" ] }, { "data": { "text/plain": [ "True" ] }, "execution_count": 57, "metadata": {}, "output_type": "execute_result" } ], "source": [ "### BEGIN SOLUTION\n", "\n", "#Skip for tests\n", "if not os.getenv(\"DEBUG\"):\n", " fr.apply(pose)\n", " \n", "pose.dump_pdb(\"outputs/2r0l_cart_rel_cdrs.pdb\")\n", "\n", "### END SOLUTION" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Regional Relax - Classic\n", "\n", "Now lets do the the classic way. Were going to take advantage of the fact that we have an Antibody here.\n", "\n", "We need to create our FoldTree and apply it to our pose before we minimize. We are going to make an AntibodyInfo object that will allow us to do this easier. Otherwise, we need to know the starting/end points of the CDR loop we are interested in. If you are interested in Antibodies, there is an Antibody Workshop later as well that will use some of the tools you have learned here. \n", "\n", "We will also use the function `fold_tree_from_loops` that is part of the loop modeling framework - also covered in later workshops. Rosetta can be difficult for sure, but the ability to use all of the different libraries in Rosetta can be a powerful tool. " ] }, { "cell_type": "code", "execution_count": 58, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mprotocols.loops.loops_main: \u001b[0mAdded cutpoint variant to residue 137\n", "\u001b[0mprotocols.loops.loops_main: \u001b[0mAdded cutpoint variant to residue 138\n", "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: sampling/antibodies/cluster_center_dihedrals.txt\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody numbering scheme definitions read successfully\n", "\u001b[0mprotocols.antibody.AntibodyNumberingParser: \u001b[0mAntibody CDR definition read successfully\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSuccessfully finished the CDR definition\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Detecting Regular CDR H3 Stem Type\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mARFWWRSFDYW\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: KINKED\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mAC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 13 Omega: TTTTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for H3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 10 Omega: TTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L1\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 11 Omega: TTTTTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L2\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 8 Omega: TTTTTTTT\n", "\u001b[0mantibody.AntibodyInfo: \u001b[0mSetting up CDR Cluster for L3\n", "\u001b[0mprotocols.antibody.cluster.CDRClusterMatcher: \u001b[0mLength: 9 Omega: TTTTTTCTT\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: repeat -520.767 0 0 0.55\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 23112 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -2366.06 2.04429 2.04429 0.011\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 21990 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -1807.48 1.12014 1.12014 0.1375\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 19735 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -1629.17 0.911645 0.911645 0.3025\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 18905 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -1472.87 0.78043 0.78043 0.55\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mMRP: 0 -1472.87 -1472.87 0.78043 0.78043\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: accept_to_best -1472.87 0.78043 0.78043 0.55\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: endrepeat -1472.87 0.78043 0.78043 0.55\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 23459 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -2417.84 1.99586 1.99586 0.011\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 22141 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -1836.37 1.21946 1.21946 0.1375\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 20724 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -1654.06 1.02747 1.02747 0.3025\n", "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n", "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 19572 rotamers at 464 positions.\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n", "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mHigh IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: ramp_repack_min -1473.13 0.960945 0.960945 0.55\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mMRP: 1 -1473.13 -1473.13 0.960945 0.960945\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: accept_to_best -1473.13 0.960945 0.960945 0.55\n", "\u001b[0mprotocols.relax.FastRelax: \u001b[0mCMD: endrepeat -1473.13 0.960945 0.960945 0.55\n", "\u001b[0mprotocols::checkpoint: \u001b[0mDeleting checkpoints of FastRelax\n" ] }, { "data": { "text/plain": [ "True" ] }, "execution_count": 58, "metadata": {}, "output_type": "execute_result" } ], "source": [ " \n", "pose = original_pose.clone()\n", "\n", "ab_info = AntibodyInfo(pose)\n", "ft = FoldTree()\n", "\n", "\n", "start = ab_info.get_CDR_start(h1, pose)\n", "stop = ab_info.get_CDR_end(h1, pose)\n", "cutpoint = int((stop-start)/2) + start\n", "cdr_loop = Loop(start, stop, cutpoint)\n", "cdr_loops = Loops()\n", "cdr_loops.add_loop(cdr_loop)\n", " \n", "fold_tree_from_loops(pose, cdr_loops, ft)\n", "pose.fold_tree(ft)\n", "original_ft = pose.fold_tree()\n", "add_cutpoint_variants(pose)\n", "\n", "#Add chainbreak term so we don't get wacky stuff. This term helps keep the peptide closed during bb movement.\n", "scorefxn_ch = scorefxn\n", "scorefxn_ch.set_weight(rosetta.core.scoring.chainbreak, 100)\n", "\n", "#Setup our FastRelax again for dihedral-space.\n", "\n", "mmf.set_cartesian(False)\n", "fr.set_scorefxn(scorefxn_ch)\n", "fr.cartesian(False)\n", "fr.set_movemap_factory(mmf)\n", "fr.max_iter(0) #Reset to default - if its 0, then we don't set it in the MinMover that FastRelax runs\n", "\n", "#Run relax here\n", "\n", "#Skip for tests\n", "if not os.getenv(\"DEBUG\"):\n", " fr.apply(pose)\n", "\n", "#Reapply the original fold tree\n", "pose.fold_tree(original_ft)\n", "\n", "pose.dump_pdb('outputs/2r0l_dih_rel_H1.pdb')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "How does the pose look? Better/worse than cartesian? No difference? How do the energies compare? Which is more general? \n", "\n", "## Conclusions\n", "\n", "That should get you started with packing/relax! We even covered some advanced topics you will see later this week such as the TaskFactory and Residue Selectors!\n", "\n", "Onto the next one!" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\n", "< [Side Chain Conformations and Dunbrack Energies](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.01-Side-Chain-Conformations-and-Dunbrack-Energies.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.03-Design-with-a-resfile-and-relax.ipynb) >

\"Open" ] } ], "metadata": { "celltoolbar": "Create Assignment", "kernelspec": { "display_name": "Python 3", "language": "python", "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": "3.7.6" }, "toc": { "base_numbering": 1, "nav_menu": {}, "number_sections": true, "sideBar": true, "skip_h1_title": false, "title_cell": "Table of Contents", "title_sidebar": "Contents", "toc_cell": false, "toc_position": {}, "toc_section_display": true, "toc_window_display": true } }, "nbformat": 4, "nbformat_minor": 1 }