Keywords: PackRotamersMover, FastRelax, MoveMapFactory, cartesian, ResidueSelector, NeighborhoodResidueSelector, CDRResidueSelector, TaskFactory, TaskOperation, InitializeFromCommandline, RestrictToRepacking, PreventRepackingRLT, OperateOnResidueSubsetOperation, SimpleMetric, SequenceMetric, clone()
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.
!pip install pyrosettacolabsetup
import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()
import pyrosetta; pyrosetta.init()
Make sure you are in the directory with the pdb files:
cd google_drive/MyDrive/student-notebooks/
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.
#Python
from pyrosetta import *
from pyrosetta.rosetta import *
from pyrosetta.teaching import *
#Core Includes
from rosetta.core.kinematics import MoveMap
from rosetta.core.kinematics import FoldTree
from rosetta.core.pack.task import TaskFactory
from rosetta.core.pack.task import operation
from rosetta.core.simple_metrics import metrics
from rosetta.core.select import residue_selector as selections
from rosetta.core import select
from rosetta.core.select.movemap import *
#Protocol Includes
from rosetta.protocols import minimization_packing as pack_min
from rosetta.protocols import relax as rel
from rosetta.protocols.antibody.residue_selector import CDRResidueSelector
from rosetta.protocols.antibody import *
from rosetta.protocols.loops import *
from rosetta.protocols.relax import FastRelax
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. We also set the input antibody numbering scheme so that Rosetta understands the nomenclature of our antibody.
Note that typically, we would add these options: -ex1
and -ex2
in order to increase the amount of rotamers
available for packing, but this will slow us down for the demo, so we are keeping this out.
init('-use_input_sc -input_ab_scheme AHo_Scheme -ignore_unrecognized_res \
-ignore_zero_occupancy false -load_PDB_components false -relax:default_repeats 2 -no_fconfig')
core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Reading fconfig.../Users/jadolfbr/.rosetta/flags/common core.init: core.init: core.init: Rosetta version: PyRosetta4.Release.python27.mac r206 2019.01+release.dbc838b6ae6 dbc838b6ae620b1293476b1bd4366ffc2facc5b5 http://www.pyrosetta.org 2019-01-03T10:31:13 core.init: command: 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 core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-153595891 seed_offset=0 real_seed=-153595891 core.init.random: RandomGenerator:init: Normal mode, seed=-153595891 RG_type=mt19937
Begin by importing a pose. Here, we are going to use an antibody from the PDB.
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
.
#Import a pose
pose = pose_from_pdb("inputs/2r0l_1_1.pdb")
original_pose = pose.clone()
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 636 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.76167 seconds. core.import_pose.import_pose: File '2r0l_1_1.pdb' automatically determined to be of type PDB core.io.pdb.pdb_reader: Parsing 0 .pdb records with unknown format to search for Rosetta-specific comments. core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 108 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER:CtermProteinFull 225 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 464 core.conformation.Conformation: Found disulfide between residues 23 88 core.conformation.Conformation: current variant for 23 CYS core.conformation.Conformation: current variant for 88 CYS core.conformation.Conformation: current variant for 23 CYD core.conformation.Conformation: current variant for 88 CYD core.conformation.Conformation: Found disulfide between residues 130 204 core.conformation.Conformation: current variant for 130 CYS core.conformation.Conformation: current variant for 204 CYS core.conformation.Conformation: current variant for 130 CYD core.conformation.Conformation: current variant for 204 CYD core.conformation.Conformation: Found disulfide between residues 250 266 core.conformation.Conformation: current variant for 250 CYS core.conformation.Conformation: current variant for 266 CYS core.conformation.Conformation: current variant for 250 CYD core.conformation.Conformation: current variant for 266 CYD core.conformation.Conformation: Found disulfide between residues 258 328 core.conformation.Conformation: current variant for 258 CYS core.conformation.Conformation: current variant for 328 CYS core.conformation.Conformation: current variant for 258 CYD core.conformation.Conformation: current variant for 328 CYD core.conformation.Conformation: Found disulfide between residues 353 422 core.conformation.Conformation: current variant for 353 CYS core.conformation.Conformation: current variant for 422 CYS core.conformation.Conformation: current variant for 353 CYD core.conformation.Conformation: current variant for 422 CYD core.conformation.Conformation: Found disulfide between residues 385 401 core.conformation.Conformation: current variant for 385 CYS core.conformation.Conformation: current variant for 401 CYS core.conformation.Conformation: current variant for 385 CYD core.conformation.Conformation: current variant for 401 CYD core.conformation.Conformation: Found disulfide between residues 412 440 core.conformation.Conformation: current variant for 412 CYS core.conformation.Conformation: current variant for 440 CYS core.conformation.Conformation: current variant for 412 CYD core.conformation.Conformation: current variant for 440 CYD
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.
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.
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.
tf = TaskFactory()
tf.push_back(operation.InitializeFromCommandline())
tf.push_back(operation.RestrictToRepacking())
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.
packer = pack_min.PackRotamersMover()
packer.task_factory(tf)
#Note that we are not passing a scorefunction here. We will use the default, cmd-line scorefunction,
# which is accessed through rosetta.core.scoring.get_score_function() and part of the packer. We use use a scorefunction later.
#Run the packer. (Note this may take a few minutes)
#Skip for tests
if not os.getenv("DEBUG"):
packer.apply(pose)
#Dump the PDB
pose.dump_pdb('/outputs/2r0l_all_repack.pdb')
protocols.minimization_packing.PackRotamersMover: [ WARNING ] undefined ScoreFunction -- creating a default one core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.pack.task: Packer task: initialize from command line() basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary 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 core.pack.dunbrack.RotamerLibrary: Using 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'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.249423 seconds to load from binary core.pack.pack_rotamers: built 18337 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.
True
Lets compare the energies of the before and after pose. Any difference?
scorefxn = get_score_function()
before = scorefxn.score(original_pose)
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
Check the sequence of the pose and the original pose using either the SequenceMetric
rosetta.core.simple_metrics.metrics.SequenceMetric
(and it's calculate function) OR directly using the pose's .sequence()
function.
Make sure that the poses have the same sequence - as packing is just design using single residue rotamers.
### BEGIN SOLUTION
seq_metric = metrics.SequenceMetric()
print("Sequence:")
print(seq_metric.calculate(pose))
#OR
print("\nSequence:")
print(pose.sequence())
### END SOLUTION
Sequence: DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYTTPPTFGQGTKVEIKREVQLVESGGGLVQPGGSLRLSCAASGFTISNSGIHWVRQAPGKGLEWVGWIYPTGGATDYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFWWRSFDYWGQGTLVTVSSIIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISWGDGCGRLHKPGVYTRVANYVDWINDRIR Sequence: DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYTTPPTFGQGTKVEIKREVQLVESGGGLVQPGGSLRLSCAASGFTISNSGIHWVRQAPGKGLEWVGWIYPTGGATDYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFWWRSFDYWGQGTLVTVSSIIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISWGDGCGRLHKPGVYTRVANYVDWINDRIR
Lets pack just a single CDR loop. How do we do this? Use a TaskFactory
and a TaskOperation
.
To make things easier, we will use a ResidueSelector
to select the CDR. You will see more of this later.
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
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.
nbr_selector = selections.NeighborhoodResidueSelector()
cdr_selector = CDRResidueSelector()
cdr_selector.set_cdr(h1)
Note that h1 is what is called an enum. It is a named integer. This is better than passing around strings, and you will start to see many of these around Rosetta. They were imported when we imported the antibody namespace at the top of this workshop. Score terms such as fa_dun are also enums.
nbr_selector.set_focus_selector(cdr_selector)
nbr_selector.set_include_focus_in_subset(True)
Lets turn off packing for everything but the H1 loop and its neighbors. By using a TF, every time packing is done, we regenerate the neighbors. Using the NeighborhoodResidueSelector we actually use the pose energies object that has a list of neighbors instead of doing an N by N calculation each time!
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.
prevent_repacking_rlt = operation.PreventRepackingRLT()
#True indicates here that we are flipping the selection. So that we are turning off everything but the CDR and
# its neighbors.
prevent_subset_repacking = operation.OperateOnResidueSubset(prevent_repacking_rlt, nbr_selector, True )
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
cdr_res = []
print("CDR")
for i in select.get_residue_set_from_subset(cdr_selector.apply(pose)):
print(i)
cdr_res.append(i)
print("\nCDR+Neighbors")
for i in select.get_residue_set_from_subset(nbr_selector.apply(pose)):
if i in cdr_res:
print(i,"CDR")
else:
print(i)
CDR basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT 131 132 133 134 135 136 137 138 139 140 141 142 143 CDR+Neighbors basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT 96 109 110 111 112 113 114 115 129 130 131 CDR 132 CDR 133 CDR 134 CDR 135 CDR 136 CDR 137 CDR 138 CDR 139 CDR 140 CDR 141 CDR 142 CDR 143 CDR 144 145 155 156 157 158 159 160 161 162 163 165 167 178 180 181 182 183 184 185 186 187 203 204 205 206 207 208 212 214 215 216 268 269 270 302 304 305 306 307 308 309
pose = original_pose.clone()
tf.push_back(prevent_subset_repacking)
pack_cdrs_and_neighbors_tf = tf.clone()
packer.task_factory(tf)
Before we start, lets take a look at our PackerTask. Are we designing anything? Does this match our selection?
print(tf.create_task_and_apply_taskoperations(pose))
core.pack.task: Packer task: initialize from command line() basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT #Packer_Task resid pack? design? allowed_aas 1 FALSE FALSE 2 FALSE FALSE 3 FALSE FALSE 4 FALSE FALSE 5 FALSE FALSE 6 FALSE FALSE 7 FALSE FALSE 8 FALSE FALSE 9 FALSE FALSE 10 FALSE FALSE 11 FALSE FALSE 12 FALSE FALSE 13 FALSE FALSE 14 FALSE FALSE 15 FALSE FALSE 16 FALSE FALSE 17 FALSE FALSE 18 FALSE FALSE 19 FALSE FALSE 20 FALSE FALSE 21 FALSE FALSE 22 FALSE FALSE 23 FALSE FALSE 24 FALSE FALSE 25 FALSE FALSE 26 FALSE FALSE 27 FALSE FALSE 28 FALSE FALSE 29 FALSE FALSE 30 FALSE FALSE 31 FALSE FALSE 32 FALSE FALSE 33 FALSE FALSE 34 FALSE FALSE 35 FALSE FALSE 36 FALSE FALSE 37 FALSE FALSE 38 FALSE FALSE 39 FALSE FALSE 40 FALSE FALSE 41 FALSE FALSE 42 FALSE FALSE 43 FALSE FALSE 44 FALSE FALSE 45 FALSE FALSE 46 FALSE FALSE 47 FALSE FALSE 48 FALSE FALSE 49 FALSE FALSE 50 FALSE FALSE 51 FALSE FALSE 52 FALSE FALSE 53 FALSE FALSE 54 FALSE FALSE 55 FALSE FALSE 56 FALSE FALSE 57 FALSE FALSE 58 FALSE FALSE 59 FALSE FALSE 60 FALSE FALSE 61 FALSE FALSE 62 FALSE FALSE 63 FALSE FALSE 64 FALSE FALSE 65 FALSE FALSE 66 FALSE FALSE 67 FALSE FALSE 68 FALSE FALSE 69 FALSE FALSE 70 FALSE FALSE 71 FALSE FALSE 72 FALSE FALSE 73 FALSE FALSE 74 FALSE FALSE 75 FALSE FALSE 76 FALSE FALSE 77 FALSE FALSE 78 FALSE FALSE 79 FALSE FALSE 80 FALSE FALSE 81 FALSE FALSE 82 FALSE FALSE 83 FALSE FALSE 84 FALSE FALSE 85 FALSE FALSE 86 FALSE FALSE 87 FALSE FALSE 88 FALSE FALSE 89 FALSE FALSE 90 FALSE FALSE 91 FALSE FALSE 92 FALSE FALSE 93 FALSE FALSE 94 FALSE FALSE 95 FALSE FALSE 96 TRUE FALSE PRO 97 FALSE FALSE 98 FALSE FALSE 99 FALSE FALSE 100 FALSE FALSE 101 FALSE FALSE 102 FALSE FALSE 103 FALSE FALSE 104 FALSE FALSE 105 FALSE FALSE 106 FALSE FALSE 107 FALSE FALSE 108 FALSE FALSE 109 TRUE FALSE GLU:NtermProteinFull 110 TRUE FALSE VAL 111 TRUE FALSE GLN 112 TRUE FALSE LEU 113 TRUE FALSE VAL 114 TRUE FALSE GLU 115 TRUE FALSE SER 116 FALSE FALSE 117 FALSE FALSE 118 FALSE FALSE 119 FALSE FALSE 120 FALSE FALSE 121 FALSE FALSE 122 FALSE FALSE 123 FALSE FALSE 124 FALSE FALSE 125 FALSE FALSE 126 FALSE FALSE 127 FALSE FALSE 128 FALSE FALSE 129 TRUE FALSE SER 130 TRUE FALSE CYS:disulfide 131 FALSE FALSE 132 FALSE FALSE 133 FALSE FALSE 134 FALSE FALSE 135 FALSE FALSE 136 FALSE FALSE 137 FALSE FALSE 138 FALSE FALSE 139 FALSE FALSE 140 FALSE FALSE 141 FALSE FALSE 142 FALSE FALSE 143 FALSE FALSE 144 TRUE FALSE TRP 145 TRUE FALSE VAL 146 FALSE FALSE 147 FALSE FALSE 148 FALSE FALSE 149 FALSE FALSE 150 FALSE FALSE 151 FALSE FALSE 152 FALSE FALSE 153 FALSE FALSE 154 FALSE FALSE 155 TRUE FALSE TRP 156 TRUE FALSE VAL 157 TRUE FALSE GLY 158 TRUE FALSE TRP 159 TRUE FALSE ILE 160 TRUE FALSE TYR 161 TRUE FALSE PRO 162 TRUE FALSE THR 163 TRUE FALSE GLY 164 FALSE FALSE 165 TRUE FALSE ALA 166 FALSE FALSE 167 TRUE FALSE ASP 168 FALSE FALSE 169 FALSE FALSE 170 FALSE FALSE 171 FALSE FALSE 172 FALSE FALSE 173 FALSE FALSE 174 FALSE FALSE 175 FALSE FALSE 176 FALSE FALSE 177 FALSE FALSE 178 TRUE FALSE ILE 179 FALSE FALSE 180 TRUE FALSE ALA 181 TRUE FALSE ASP 182 TRUE FALSE THR 183 TRUE FALSE SER 184 TRUE FALSE LYS 185 TRUE FALSE ASN 186 TRUE FALSE THR 187 TRUE FALSE ALA 188 FALSE FALSE 189 FALSE FALSE 190 FALSE FALSE 191 FALSE FALSE 192 FALSE FALSE 193 FALSE FALSE 194 FALSE FALSE 195 FALSE FALSE 196 FALSE FALSE 197 FALSE FALSE 198 FALSE FALSE 199 FALSE FALSE 200 FALSE FALSE 201 FALSE FALSE 202 FALSE FALSE 203 TRUE FALSE TYR 204 TRUE FALSE CYS:disulfide 205 TRUE FALSE ALA 206 TRUE FALSE ARG 207 TRUE FALSE PHE 208 TRUE FALSE TRP 209 FALSE FALSE 210 FALSE FALSE 211 FALSE FALSE 212 TRUE FALSE PHE 213 FALSE FALSE 214 TRUE FALSE TYR 215 TRUE FALSE TRP 216 TRUE FALSE GLY 217 FALSE FALSE 218 FALSE FALSE 219 FALSE FALSE 220 FALSE FALSE 221 FALSE FALSE 222 FALSE FALSE 223 FALSE FALSE 224 FALSE FALSE 225 FALSE FALSE 226 FALSE FALSE 227 FALSE FALSE 228 FALSE FALSE 229 FALSE FALSE 230 FALSE FALSE 231 FALSE FALSE 232 FALSE FALSE 233 FALSE FALSE 234 FALSE FALSE 235 FALSE FALSE 236 FALSE FALSE 237 FALSE FALSE 238 FALSE FALSE 239 FALSE FALSE 240 FALSE FALSE 241 FALSE FALSE 242 FALSE FALSE 243 FALSE FALSE 244 FALSE FALSE 245 FALSE FALSE 246 FALSE FALSE 247 FALSE FALSE 248 FALSE FALSE 249 FALSE FALSE 250 FALSE FALSE 251 FALSE FALSE 252 FALSE FALSE 253 FALSE FALSE 254 FALSE FALSE 255 FALSE FALSE 256 FALSE FALSE 257 FALSE FALSE 258 FALSE FALSE 259 FALSE FALSE 260 FALSE FALSE 261 FALSE FALSE 262 FALSE FALSE 263 FALSE FALSE 264 FALSE FALSE 265 FALSE FALSE 266 FALSE FALSE 267 FALSE FALSE 268 TRUE FALSE SER 269 TRUE FALSE HIS,HIS_D 270 TRUE FALSE SER 271 FALSE FALSE 272 FALSE FALSE 273 FALSE FALSE 274 FALSE FALSE 275 FALSE FALSE 276 FALSE FALSE 277 FALSE FALSE 278 FALSE FALSE 279 FALSE FALSE 280 FALSE FALSE 281 FALSE FALSE 282 FALSE FALSE 283 FALSE FALSE 284 FALSE FALSE 285 FALSE FALSE 286 FALSE FALSE 287 FALSE FALSE 288 FALSE FALSE 289 FALSE FALSE 290 FALSE FALSE 291 FALSE FALSE 292 FALSE FALSE 293 FALSE FALSE 294 FALSE FALSE 295 FALSE FALSE 296 FALSE FALSE 297 FALSE FALSE 298 FALSE FALSE 299 FALSE FALSE 300 FALSE FALSE 301 FALSE FALSE 302 TRUE FALSE PRO 303 FALSE FALSE 304 TRUE FALSE THR 305 TRUE FALSE LEU 306 TRUE FALSE TYR 307 TRUE FALSE SER 308 TRUE FALSE VAL 309 TRUE FALSE PHE 310 FALSE FALSE 311 FALSE FALSE 312 FALSE FALSE 313 FALSE FALSE 314 FALSE FALSE 315 FALSE FALSE 316 FALSE FALSE 317 FALSE FALSE 318 FALSE FALSE 319 FALSE FALSE 320 FALSE FALSE 321 FALSE FALSE 322 FALSE FALSE 323 FALSE FALSE 324 FALSE FALSE 325 FALSE FALSE 326 FALSE FALSE 327 FALSE FALSE 328 FALSE FALSE 329 FALSE FALSE 330 FALSE FALSE 331 FALSE FALSE 332 FALSE FALSE 333 FALSE FALSE 334 FALSE FALSE 335 FALSE FALSE 336 FALSE FALSE 337 FALSE FALSE 338 FALSE FALSE 339 FALSE FALSE 340 FALSE FALSE 341 FALSE FALSE 342 FALSE FALSE 343 FALSE FALSE 344 FALSE FALSE 345 FALSE FALSE 346 FALSE FALSE 347 FALSE FALSE 348 FALSE FALSE 349 FALSE FALSE 350 FALSE FALSE 351 FALSE FALSE 352 FALSE FALSE 353 FALSE FALSE 354 FALSE FALSE 355 FALSE FALSE 356 FALSE FALSE 357 FALSE FALSE 358 FALSE FALSE 359 FALSE FALSE 360 FALSE FALSE 361 FALSE FALSE 362 FALSE FALSE 363 FALSE FALSE 364 FALSE FALSE 365 FALSE FALSE 366 FALSE FALSE 367 FALSE FALSE 368 FALSE FALSE 369 FALSE FALSE 370 FALSE FALSE 371 FALSE FALSE 372 FALSE FALSE 373 FALSE FALSE 374 FALSE FALSE 375 FALSE FALSE 376 FALSE FALSE 377 FALSE FALSE 378 FALSE FALSE 379 FALSE FALSE 380 FALSE FALSE 381 FALSE FALSE 382 FALSE FALSE 383 FALSE FALSE 384 FALSE FALSE 385 FALSE FALSE 386 FALSE FALSE 387 FALSE FALSE 388 FALSE FALSE 389 FALSE FALSE 390 FALSE FALSE 391 FALSE FALSE 392 FALSE FALSE 393 FALSE FALSE 394 FALSE FALSE 395 FALSE FALSE 396 FALSE FALSE 397 FALSE FALSE 398 FALSE FALSE 399 FALSE FALSE 400 FALSE FALSE 401 FALSE FALSE 402 FALSE FALSE 403 FALSE FALSE 404 FALSE FALSE 405 FALSE FALSE 406 FALSE FALSE 407 FALSE FALSE 408 FALSE FALSE 409 FALSE FALSE 410 FALSE FALSE 411 FALSE FALSE 412 FALSE FALSE 413 FALSE FALSE 414 FALSE FALSE 415 FALSE FALSE 416 FALSE FALSE 417 FALSE FALSE 418 FALSE FALSE 419 FALSE FALSE 420 FALSE FALSE 421 FALSE FALSE 422 FALSE FALSE 423 FALSE FALSE 424 FALSE FALSE 425 FALSE FALSE 426 FALSE FALSE 427 FALSE FALSE 428 FALSE FALSE 429 FALSE FALSE 430 FALSE FALSE 431 FALSE FALSE 432 FALSE FALSE 433 FALSE FALSE 434 FALSE FALSE 435 FALSE FALSE 436 FALSE FALSE 437 FALSE FALSE 438 FALSE FALSE 439 FALSE FALSE 440 FALSE FALSE 441 FALSE FALSE 442 FALSE FALSE 443 FALSE FALSE 444 FALSE FALSE 445 FALSE FALSE 446 FALSE FALSE 447 FALSE FALSE 448 FALSE FALSE 449 FALSE FALSE 450 FALSE FALSE 451 FALSE FALSE 452 FALSE FALSE 453 FALSE FALSE 454 FALSE FALSE 455 FALSE FALSE 456 FALSE FALSE 457 FALSE FALSE 458 FALSE FALSE 459 FALSE FALSE 460 FALSE FALSE 461 FALSE FALSE 462 FALSE FALSE 463 FALSE FALSE 464 FALSE FALSE
Now lets Run the packer and dump the PDB.
Note how many rotamers were used and how many positions were done. Now run it again. Have those numbers changed? Why?
### BEGIN SOLUTION
#Skip for tests
if not os.getenv("DEBUG"):
packer.apply(pose)
pose.dump_pdb("outputs/2r0l_cdr_repack.pdb")
### END SOLUTION
core.pack.task: Packer task: initialize from command line() basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT core.pack.pack_rotamers: built 1952 rotamers at 52 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
True
Lets design this CDR. We already almost everything we need created, so lets do this!!
Note, since we added the RestrictToRepacking TaskOperation to our original TaskFactory
, we need to reset (clear) it.
pose = original_pose.clone()
tf.clear()
tf.push_back(operation.InitializeFromCommandline())
tf.push_back(prevent_subset_repacking)
#Turn off design of neighbors
nbr_selector2 = selections.NeighborhoodResidueSelector()
nbr_selector2.set_focus_selector(cdr_selector)
nbr_selector2.set_include_focus_in_subset(False)
restrict_to_repack = operation.RestrictToRepackingRLT()
prevent_nbr_design = operation.OperateOnResidueSubset(restrict_to_repack, nbr_selector2, False )
tf.push_back(prevent_nbr_design)
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.
print(tf.create_task_and_apply_taskoperations(pose))
core.pack.task: Packer task: initialize from command line() basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT #Packer_Task resid pack? design? allowed_aas 1 FALSE FALSE 2 FALSE FALSE 3 FALSE FALSE 4 FALSE FALSE 5 FALSE FALSE 6 FALSE FALSE 7 FALSE FALSE 8 FALSE FALSE 9 FALSE FALSE 10 FALSE FALSE 11 FALSE FALSE 12 FALSE FALSE 13 FALSE FALSE 14 FALSE FALSE 15 FALSE FALSE 16 FALSE FALSE 17 FALSE FALSE 18 FALSE FALSE 19 FALSE FALSE 20 FALSE FALSE 21 FALSE FALSE 22 FALSE FALSE 23 FALSE FALSE 24 FALSE FALSE 25 FALSE FALSE 26 FALSE FALSE 27 FALSE FALSE 28 FALSE FALSE 29 FALSE FALSE 30 FALSE FALSE 31 FALSE FALSE 32 FALSE FALSE 33 FALSE FALSE 34 FALSE FALSE 35 FALSE FALSE 36 FALSE FALSE 37 FALSE FALSE 38 FALSE FALSE 39 FALSE FALSE 40 FALSE FALSE 41 FALSE FALSE 42 FALSE FALSE 43 FALSE FALSE 44 FALSE FALSE 45 FALSE FALSE 46 FALSE FALSE 47 FALSE FALSE 48 FALSE FALSE 49 FALSE FALSE 50 FALSE FALSE 51 FALSE FALSE 52 FALSE FALSE 53 FALSE FALSE 54 FALSE FALSE 55 FALSE FALSE 56 FALSE FALSE 57 FALSE FALSE 58 FALSE FALSE 59 FALSE FALSE 60 FALSE FALSE 61 FALSE FALSE 62 FALSE FALSE 63 FALSE FALSE 64 FALSE FALSE 65 FALSE FALSE 66 FALSE FALSE 67 FALSE FALSE 68 FALSE FALSE 69 FALSE FALSE 70 FALSE FALSE 71 FALSE FALSE 72 FALSE FALSE 73 FALSE FALSE 74 FALSE FALSE 75 FALSE FALSE 76 FALSE FALSE 77 FALSE FALSE 78 FALSE FALSE 79 FALSE FALSE 80 FALSE FALSE 81 FALSE FALSE 82 FALSE FALSE 83 FALSE FALSE 84 FALSE FALSE 85 FALSE FALSE 86 FALSE FALSE 87 FALSE FALSE 88 FALSE FALSE 89 FALSE FALSE 90 FALSE FALSE 91 FALSE FALSE 92 FALSE FALSE 93 FALSE FALSE 94 FALSE FALSE 95 FALSE FALSE 96 TRUE FALSE PRO 97 FALSE FALSE 98 FALSE FALSE 99 FALSE FALSE 100 FALSE FALSE 101 FALSE FALSE 102 FALSE FALSE 103 FALSE FALSE 104 FALSE FALSE 105 FALSE FALSE 106 FALSE FALSE 107 FALSE FALSE 108 FALSE FALSE 109 TRUE FALSE GLU:NtermProteinFull 110 TRUE FALSE VAL 111 TRUE FALSE GLN 112 TRUE FALSE LEU 113 TRUE FALSE VAL 114 TRUE FALSE GLU 115 TRUE FALSE SER 116 FALSE FALSE 117 FALSE FALSE 118 FALSE FALSE 119 FALSE FALSE 120 FALSE FALSE 121 FALSE FALSE 122 FALSE FALSE 123 FALSE FALSE 124 FALSE FALSE 125 FALSE FALSE 126 FALSE FALSE 127 FALSE FALSE 128 FALSE FALSE 129 TRUE FALSE SER 130 TRUE FALSE CYS:disulfide 131 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 132 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 133 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 134 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 135 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 136 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 137 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 138 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 139 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 140 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 141 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 142 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 143 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 144 TRUE FALSE TRP 145 TRUE FALSE VAL 146 FALSE FALSE 147 FALSE FALSE 148 FALSE FALSE 149 FALSE FALSE 150 FALSE FALSE 151 FALSE FALSE 152 FALSE FALSE 153 FALSE FALSE 154 FALSE FALSE 155 TRUE FALSE TRP 156 TRUE FALSE VAL 157 TRUE FALSE GLY 158 TRUE FALSE TRP 159 TRUE FALSE ILE 160 TRUE FALSE TYR 161 TRUE FALSE PRO 162 TRUE FALSE THR 163 TRUE FALSE GLY 164 FALSE FALSE 165 TRUE FALSE ALA 166 FALSE FALSE 167 TRUE FALSE ASP 168 FALSE FALSE 169 FALSE FALSE 170 FALSE FALSE 171 FALSE FALSE 172 FALSE FALSE 173 FALSE FALSE 174 FALSE FALSE 175 FALSE FALSE 176 FALSE FALSE 177 FALSE FALSE 178 TRUE FALSE ILE 179 FALSE FALSE 180 TRUE FALSE ALA 181 TRUE FALSE ASP 182 TRUE FALSE THR 183 TRUE FALSE SER 184 TRUE FALSE LYS 185 TRUE FALSE ASN 186 TRUE FALSE THR 187 TRUE FALSE ALA 188 FALSE FALSE 189 FALSE FALSE 190 FALSE FALSE 191 FALSE FALSE 192 FALSE FALSE 193 FALSE FALSE 194 FALSE FALSE 195 FALSE FALSE 196 FALSE FALSE 197 FALSE FALSE 198 FALSE FALSE 199 FALSE FALSE 200 FALSE FALSE 201 FALSE FALSE 202 FALSE FALSE 203 TRUE FALSE TYR 204 TRUE FALSE CYS:disulfide 205 TRUE FALSE ALA 206 TRUE FALSE ARG 207 TRUE FALSE PHE 208 TRUE FALSE TRP 209 FALSE FALSE 210 FALSE FALSE 211 FALSE FALSE 212 TRUE FALSE PHE 213 FALSE FALSE 214 TRUE FALSE TYR 215 TRUE FALSE TRP 216 TRUE FALSE GLY 217 FALSE FALSE 218 FALSE FALSE 219 FALSE FALSE 220 FALSE FALSE 221 FALSE FALSE 222 FALSE FALSE 223 FALSE FALSE 224 FALSE FALSE 225 FALSE FALSE 226 FALSE FALSE 227 FALSE FALSE 228 FALSE FALSE 229 FALSE FALSE 230 FALSE FALSE 231 FALSE FALSE 232 FALSE FALSE 233 FALSE FALSE 234 FALSE FALSE 235 FALSE FALSE 236 FALSE FALSE 237 FALSE FALSE 238 FALSE FALSE 239 FALSE FALSE 240 FALSE FALSE 241 FALSE FALSE 242 FALSE FALSE 243 FALSE FALSE 244 FALSE FALSE 245 FALSE FALSE 246 FALSE FALSE 247 FALSE FALSE 248 FALSE FALSE 249 FALSE FALSE 250 FALSE FALSE 251 FALSE FALSE 252 FALSE FALSE 253 FALSE FALSE 254 FALSE FALSE 255 FALSE FALSE 256 FALSE FALSE 257 FALSE FALSE 258 FALSE FALSE 259 FALSE FALSE 260 FALSE FALSE 261 FALSE FALSE 262 FALSE FALSE 263 FALSE FALSE 264 FALSE FALSE 265 FALSE FALSE 266 FALSE FALSE 267 FALSE FALSE 268 TRUE FALSE SER 269 TRUE FALSE HIS,HIS_D 270 TRUE FALSE SER 271 FALSE FALSE 272 FALSE FALSE 273 FALSE FALSE 274 FALSE FALSE 275 FALSE FALSE 276 FALSE FALSE 277 FALSE FALSE 278 FALSE FALSE 279 FALSE FALSE 280 FALSE FALSE 281 FALSE FALSE 282 FALSE FALSE 283 FALSE FALSE 284 FALSE FALSE 285 FALSE FALSE 286 FALSE FALSE 287 FALSE FALSE 288 FALSE FALSE 289 FALSE FALSE 290 FALSE FALSE 291 FALSE FALSE 292 FALSE FALSE 293 FALSE FALSE 294 FALSE FALSE 295 FALSE FALSE 296 FALSE FALSE 297 FALSE FALSE 298 FALSE FALSE 299 FALSE FALSE 300 FALSE FALSE 301 FALSE FALSE 302 TRUE FALSE PRO 303 FALSE FALSE 304 TRUE FALSE THR 305 TRUE FALSE LEU 306 TRUE FALSE TYR 307 TRUE FALSE SER 308 TRUE FALSE VAL 309 TRUE FALSE PHE 310 FALSE FALSE 311 FALSE FALSE 312 FALSE FALSE 313 FALSE FALSE 314 FALSE FALSE 315 FALSE FALSE 316 FALSE FALSE 317 FALSE FALSE 318 FALSE FALSE 319 FALSE FALSE 320 FALSE FALSE 321 FALSE FALSE 322 FALSE FALSE 323 FALSE FALSE 324 FALSE FALSE 325 FALSE FALSE 326 FALSE FALSE 327 FALSE FALSE 328 FALSE FALSE 329 FALSE FALSE 330 FALSE FALSE 331 FALSE FALSE 332 FALSE FALSE 333 FALSE FALSE 334 FALSE FALSE 335 FALSE FALSE 336 FALSE FALSE 337 FALSE FALSE 338 FALSE FALSE 339 FALSE FALSE 340 FALSE FALSE 341 FALSE FALSE 342 FALSE FALSE 343 FALSE FALSE 344 FALSE FALSE 345 FALSE FALSE 346 FALSE FALSE 347 FALSE FALSE 348 FALSE FALSE 349 FALSE FALSE 350 FALSE FALSE 351 FALSE FALSE 352 FALSE FALSE 353 FALSE FALSE 354 FALSE FALSE 355 FALSE FALSE 356 FALSE FALSE 357 FALSE FALSE 358 FALSE FALSE 359 FALSE FALSE 360 FALSE FALSE 361 FALSE FALSE 362 FALSE FALSE 363 FALSE FALSE 364 FALSE FALSE 365 FALSE FALSE 366 FALSE FALSE 367 FALSE FALSE 368 FALSE FALSE 369 FALSE FALSE 370 FALSE FALSE 371 FALSE FALSE 372 FALSE FALSE 373 FALSE FALSE 374 FALSE FALSE 375 FALSE FALSE 376 FALSE FALSE 377 FALSE FALSE 378 FALSE FALSE 379 FALSE FALSE 380 FALSE FALSE 381 FALSE FALSE 382 FALSE FALSE 383 FALSE FALSE 384 FALSE FALSE 385 FALSE FALSE 386 FALSE FALSE 387 FALSE FALSE 388 FALSE FALSE 389 FALSE FALSE 390 FALSE FALSE 391 FALSE FALSE 392 FALSE FALSE 393 FALSE FALSE 394 FALSE FALSE 395 FALSE FALSE 396 FALSE FALSE 397 FALSE FALSE 398 FALSE FALSE 399 FALSE FALSE 400 FALSE FALSE 401 FALSE FALSE 402 FALSE FALSE 403 FALSE FALSE 404 FALSE FALSE 405 FALSE FALSE 406 FALSE FALSE 407 FALSE FALSE 408 FALSE FALSE 409 FALSE FALSE 410 FALSE FALSE 411 FALSE FALSE 412 FALSE FALSE 413 FALSE FALSE 414 FALSE FALSE 415 FALSE FALSE 416 FALSE FALSE 417 FALSE FALSE 418 FALSE FALSE 419 FALSE FALSE 420 FALSE FALSE 421 FALSE FALSE 422 FALSE FALSE 423 FALSE FALSE 424 FALSE FALSE 425 FALSE FALSE 426 FALSE FALSE 427 FALSE FALSE 428 FALSE FALSE 429 FALSE FALSE 430 FALSE FALSE 431 FALSE FALSE 432 FALSE FALSE 433 FALSE FALSE 434 FALSE FALSE 435 FALSE FALSE 436 FALSE FALSE 437 FALSE FALSE 438 FALSE FALSE 439 FALSE FALSE 440 FALSE FALSE 441 FALSE FALSE 442 FALSE FALSE 443 FALSE FALSE 444 FALSE FALSE 445 FALSE FALSE 446 FALSE FALSE 447 FALSE FALSE 448 FALSE FALSE 449 FALSE FALSE 450 FALSE FALSE 451 FALSE FALSE 452 FALSE FALSE 453 FALSE FALSE 454 FALSE FALSE 455 FALSE FALSE 456 FALSE FALSE 457 FALSE FALSE 458 FALSE FALSE 459 FALSE FALSE 460 FALSE FALSE 461 FALSE FALSE 462 FALSE FALSE 463 FALSE FALSE 464 FALSE FALSE
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.
Dump the PDB and take a look.
### BEGIN SOLUTION
packer.task_factory(tf)
#Skip for tests
if not os.getenv("DEBUG"):
packer.apply(pose)
pose.dump_pdb("outputs/2r0l_cdr_design.pdb")
### END SOLUTION
core.pack.task: Packer task: initialize from command line() basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT core.pack.pack_rotamers: built 15803 rotamers at 65 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type.
True
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.
pose = original_pose.clone()
fr = FastRelax()
#Here, we have to set a scorefunction or we segfault.
# Error checking is important, and protocols should use a default scorefunction. We will manage.
fr.set_scorefxn(scorefxn)
#Lets run this. This takes a very long time, so we are going decrease the amount of minimization cycles we use.
# This is generally only recommended for cartesian, but we just want everything to run fast at the moment.
fr.max_iter(100)
#Run the code
#Dump the pdb and take a look.
### BEGIN SOLUTION
#Skip for tests
if not os.getenv("DEBUG"):
fr.apply(pose)
pose.dump_pdb("outputs/2r0l_relaxed.pdb")
### END SOLUTION
protocols.relax.FastRelax: CMD: repeat -520.742 0 0 0.55 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 23112 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -2274.11 2.36629 2.36629 0.011 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 22197 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -1775.66 1.29813 1.29813 0.1375 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 20679 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -1636.07 0.885842 0.885842 0.3025 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 18762 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -1474.81 0.74887 0.74887 0.55 protocols.relax.FastRelax: MRP: 0 -1474.81 -1474.81 0.74887 0.74887 protocols.relax.FastRelax: CMD: accept_to_best -1474.81 0.74887 0.74887 0.55 protocols.relax.FastRelax: CMD: endrepeat -1474.81 0.74887 0.74887 0.55 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 22507 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -2379.43 2.67173 2.67173 0.011 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 22466 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -1819.36 1.38682 1.38682 0.1375 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 20203 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -1647.92 1.06563 1.06563 0.3025 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 18909 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -1479.55 0.872626 0.872626 0.55 protocols.relax.FastRelax: MRP: 1 -1479.55 -1479.55 0.872626 0.872626 protocols.relax.FastRelax: CMD: accept_to_best -1479.55 0.872626 0.872626 0.55 protocols.relax.FastRelax: CMD: endrepeat -1479.55 0.872626 0.872626 0.55 protocols::checkpoint: Deleting checkpoints of FastRelax
True
Check the energy difference here once again. Note how low it is compared to simply packing
delta = ?
### BEGIN SOLUTION
print("relaxed ",scorefxn(pose))
print("original",scorefxn(original_pose))
delta = scorefxn(pose) - scorefxn(original_pose)
print("delta ",delta)
### END SOLUTION
relaxed -1479.54882708 original -520.742210502 delta -958.806616578
So that was fun, but what we really want is to optimize regions of the protein that we care about. This can be tricky, so to start off, lets do the basic thing and see what happens.
We will use a MoveMapFactory
, which allows us to use ResidueSelectors
.
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
The default is to have everything OFF first, and turn specific things on.
pose = original_pose.clone()
mmf = MoveMapFactory()
#mm_enable and mm_disable are Enums (numbered variables) that come when we import the MMF
mmf.add_bb_action(mm_enable, cdr_selector)
#mmf.add_chi_action(mm_enable, cdr_selector) We are taking this out for speed.
mm = mmf.create_movemap_from_pose(pose)
basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT
Lets take a look at our MoveMap
that the MoveMapFactory
creates. Pass the movemap to print()
We should only have a few residues there.
Here, we only want to pack the region and neighbors. NOT all 500 residues!
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.
fr.set_movemap_factory(mmf)
fr.set_task_factory(pack_cdrs_and_neighbors_tf)
Run this, take a break and then lets see the results. Dump the pose and take a look at it.
### BEGIN SOLUTION
#Skip for tests
if not os.getenv("DEBUG"):
fr.apply(pose)
pose.dump_pdb("outputs/2r0l_h1_relaxed.pdb")
### END SOLUTION
basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.relax.FastRelax: CMD: repeat -520.742 0 0 0.55 core.pack.task: Packer task: initialize from command line() basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT core.pack.pack_rotamers: built 3016 rotamers at 52 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 20 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -1107.12 1.3573 1.3573 0.011 core.pack.task: Packer task: initialize from command line() basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT core.pack.pack_rotamers: built 2235 rotamers at 62 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 20 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -737.418 0.80441 0.80441 0.1375 core.pack.task: Packer task: initialize from command line() basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT core.pack.pack_rotamers: built 2103 rotamers at 57 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 20 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -765.555 0.342906 0.342906 0.3025 core.pack.task: Packer task: initialize from command line() basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT core.pack.pack_rotamers: built 2030 rotamers at 55 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 20 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -660.025 0.262438 0.262438 0.55 protocols.relax.FastRelax: MRP: 0 -660.025 -660.025 0.262438 0.262438 protocols.relax.FastRelax: CMD: accept_to_best -660.025 0.262438 0.262438 0.55 protocols.relax.FastRelax: CMD: endrepeat -660.025 0.262438 0.262438 0.55 core.pack.task: Packer task: initialize from command line() basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT core.pack.pack_rotamers: built 3000 rotamers at 54 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 20 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -1161.16 1.43343 1.43343 0.011 core.pack.task: Packer task: initialize from command line() basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT core.pack.pack_rotamers: built 2284 rotamers at 60 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 20 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -796.449 0.632186 0.632186 0.1375 core.pack.task: Packer task: initialize from command line() basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT core.pack.pack_rotamers: built 2015 rotamers at 53 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 20 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -747.137 0.590596 0.590596 0.3025 core.pack.task: Packer task: initialize from command line() basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT core.pack.pack_rotamers: built 1926 rotamers at 56 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 20 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -676.771 0.355995 0.355995 0.55 protocols.relax.FastRelax: MRP: 1 -676.771 -676.771 0.355995 0.355995 protocols.relax.FastRelax: CMD: accept_to_best -676.771 0.355995 0.355995 0.55 protocols.relax.FastRelax: CMD: endrepeat -676.771 0.355995 0.355995 0.55 protocols::checkpoint: Deleting checkpoints of FastRelax
True
What is wrong with this Pose???
Okay, so we know whats wrong here, right? Right? The pose is moving too much where we don't want it. This is due to the FoldTree 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.
Lets do the easier of the two - cartesian!
pose = original_pose.clone()
cart_sf = create_score_function("ref2015_cart")
mmf.set_cartesian(True)
fr.set_movemap_factory(mmf)
fr.set_scorefxn(cart_sf)
fr.cartesian(True)
#This is a general recommendation for cartesian minimization - it lowers the number of maximum cycles.
# More than this only increases time of protocol, but has little effect on energies/structure
fr.max_iter(200)
core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40 basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt core.scoring.CartesianBondedEnergy: Read 757 bb-independent lengths. basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt core.scoring.CartesianBondedEnergy: Read 1456 bb-independent angles. basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt core.scoring.CartesianBondedEnergy: Read 1 bb-independent torsions. basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt core.scoring.CartesianBondedEnergy: Read 2197 bb-independent improper tors.
Run relax Lets dump the pose and take a look again. Does this look better? How are the energies?
### BEGIN SOLUTION
#Skip for tests
if not os.getenv("DEBUG"):
fr.apply(pose)
pose.dump_pdb("outputs/2r0l_cart_rel_cdrs.pdb")
### END SOLUTION
basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (464) protocols.relax.FastRelax: CMD: repeat -230.749 0 0 0.55 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 23112 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 23 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 88 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 130 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 204 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 250 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 258 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 266 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 328 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 353 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 385 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 401 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 412 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 422 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 440 BRANCH 1 core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -2393.05 0.88128 0.88128 0.011 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 22793 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 23 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 88 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 130 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 204 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 250 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 258 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 266 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 328 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 353 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 385 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 401 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 412 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 422 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 440 BRANCH 1 core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -1944.4 0.721666 0.721666 0.1375 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 20680 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 23 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 88 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 130 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 204 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 250 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 258 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 266 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 328 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 353 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 385 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 401 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 412 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 422 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 440 BRANCH 1 core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -1782.16 0.65455 0.65455 0.3025 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 19414 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 23 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 88 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 130 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 204 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 250 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 258 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 266 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 328 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 353 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 385 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 401 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 412 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 422 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 440 BRANCH 1 core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -1624.65 0.592299 0.592299 0.55 protocols.relax.FastRelax: MRP: 0 -1624.65 -1624.65 0.592299 0.592299 protocols.relax.FastRelax: CMD: accept_to_best -1624.65 0.592299 0.592299 0.55 protocols.relax.FastRelax: CMD: endrepeat -1624.65 0.592299 0.592299 0.55 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 24179 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 23 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 88 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 130 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 204 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 250 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 258 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 266 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 328 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 353 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 385 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 401 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 412 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 422 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 440 BRANCH 1 core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -2526.51 1.19733 1.19733 0.011 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 22124 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 23 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 88 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 130 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 204 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 250 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 258 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 266 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 328 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 353 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 385 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 401 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 412 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 422 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 440 BRANCH 1 core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -2011.26 0.96739 0.96739 0.1375 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 20397 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 23 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 88 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 130 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 204 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 250 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 258 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 266 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 328 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 353 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 385 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 401 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 412 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 422 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 440 BRANCH 1 core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -1820.1 0.848976 0.848976 0.3025 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 19350 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 23 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 88 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 130 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 204 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 250 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 258 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 266 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 328 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 353 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 385 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 401 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 412 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 422 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 440 BRANCH 1 core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED! protocols.relax.FastRelax: CMD: ramp_repack_min -1652.52 0.756863 0.756863 0.55 protocols.relax.FastRelax: MRP: 1 -1652.52 -1652.52 0.756863 0.756863 protocols.relax.FastRelax: CMD: accept_to_best -1652.52 0.756863 0.756863 0.55 protocols.relax.FastRelax: CMD: endrepeat -1652.52 0.756863 0.756863 0.55 protocols::checkpoint: Deleting checkpoints of FastRelax
True
Now lets do the the classic way. Were going to take advantage of the fact that we have an Antibody here.
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.
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.
pose = original_pose.clone()
ab_info = AntibodyInfo(pose)
ft = FoldTree()
start = ab_info.get_CDR_start(h1, pose)
stop = ab_info.get_CDR_end(h1, pose)
cutpoint = int((stop-start)/2) + start
cdr_loop = Loop(start, stop, cutpoint)
cdr_loops = Loops()
cdr_loops.add_loop(cdr_loop)
fold_tree_from_loops(pose, cdr_loops, ft)
pose.fold_tree(ft)
original_ft = pose.fold_tree()
add_cutpoint_variants(pose)
#Add chainbreak term so we don't get wacky stuff. This term helps keep the peptide closed during bb movement.
scorefxn_ch = scorefxn
scorefxn_ch.set_weight(rosetta.core.scoring.chainbreak, 100)
#Setup our FastRelax again for dihedral-space.
mmf.set_cartesian(False)
fr.set_scorefxn(scorefxn_ch)
fr.cartesian(False)
fr.set_movemap_factory(mmf)
fr.max_iter(0) #Reset to default - if its 0, then we don't set it in the MinMover that FastRelax runs
#Run relax here
#Skip for tests
if not os.getenv("DEBUG"):
fr.apply(pose)
#Reapply the original fold tree
pose.fold_tree(original_ft)
pose.dump_pdb('outputs/2r0l_dih_rel_H1.pdb')
basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.loops.loops_main: Added cutpoint variant to residue 137 protocols.loops.loops_main: Added cutpoint variant to residue 138 basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARFWWRSFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.relax.FastRelax: CMD: repeat -520.767 0 0 0.55 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 23112 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. protocols.relax.FastRelax: CMD: ramp_repack_min -2366.06 2.04429 2.04429 0.011 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 21990 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. protocols.relax.FastRelax: CMD: ramp_repack_min -1807.48 1.12014 1.12014 0.1375 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 19735 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. protocols.relax.FastRelax: CMD: ramp_repack_min -1629.17 0.911645 0.911645 0.3025 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 18905 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. protocols.relax.FastRelax: CMD: ramp_repack_min -1472.87 0.78043 0.78043 0.55 protocols.relax.FastRelax: MRP: 0 -1472.87 -1472.87 0.78043 0.78043 protocols.relax.FastRelax: CMD: accept_to_best -1472.87 0.78043 0.78043 0.55 protocols.relax.FastRelax: CMD: endrepeat -1472.87 0.78043 0.78043 0.55 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 23459 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. protocols.relax.FastRelax: CMD: ramp_repack_min -2417.84 1.99586 1.99586 0.011 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 22141 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. protocols.relax.FastRelax: CMD: ramp_repack_min -1836.37 1.21946 1.21946 0.1375 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 20724 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. protocols.relax.FastRelax: CMD: ramp_repack_min -1654.06 1.02747 1.02747 0.3025 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 19572 rotamers at 464 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: High IG memory usage (>25 MB). If this becomes an issue, consider using a different interaction graph type. protocols.relax.FastRelax: CMD: ramp_repack_min -1473.13 0.960945 0.960945 0.55 protocols.relax.FastRelax: MRP: 1 -1473.13 -1473.13 0.960945 0.960945 protocols.relax.FastRelax: CMD: accept_to_best -1473.13 0.960945 0.960945 0.55 protocols.relax.FastRelax: CMD: endrepeat -1473.13 0.960945 0.960945 0.55 protocols::checkpoint: Deleting checkpoints of FastRelax
True
How does the pose look? Better/worse than cartesian? No difference? How do the energies compare? Which is more general?
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!
Onto the next one!