This notebook contains material from PyRosetta; content is available on Github.

Packing and Relax

Keywords: PackRotamersMover, FastRelax, MoveMapFactory, cartesian, ResidueSelector, NeighborhoodResidueSelector, CDRResidueSelector, TaskFactory, TaskOperation, InitializeFromCommandline, RestrictToRepacking, PreventRepackingRLT, OperateOnResidueSubsetOperation, SimpleMetric, SequenceMetric, clone()

Overview

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.

In [ ]:
# Notebook setup
import sys
if 'google.colab' in sys.modules:
    !pip install pyrosettacolabsetup
    import pyrosettacolabsetup
    pyrosettacolabsetup.mount_pyrosetta_install()
    print ("Notebook is set for PyRosetta use in Colab.  Have fun!")

Make sure you are in the directory with the pdb files:

cd google_drive/My\ Drive/student-notebooks/

Imports

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.

In [29]:
#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

Intitlialization

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.

In [2]:
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

Import and copy pose

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.

In [3]:
#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

Setup a Normal TaskFactory

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.

In [4]:
tf = TaskFactory()
tf.push_back(operation.InitializeFromCommandline())
tf.push_back(operation.RestrictToRepacking())

Setup The Packer

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.

In [5]:
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.
Out[5]:
True

Lets compare the energies of the before and after pose. Any difference?

In [6]:
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.

In [13]:
### 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

Regional Packing

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

Make selection using the CDRResidueSelector and NeighborhoodResidueSelector

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.

In [32]:
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.

In [33]:
nbr_selector.set_focus_selector(cdr_selector)
nbr_selector.set_include_focus_in_subset(True)

Restrict to our selection

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.

In [34]:
prevent_repacking_rlt = operation.PreventRepackingRLT()
In [35]:
#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

In [36]:
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

Reset the pose

In [37]:
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?

In [38]:
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?

In [39]:
### 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
Out[39]:
True

Design

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.

In [40]:
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.

In [41]:
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 and Run

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.

In [42]:
### 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.
Out[42]:
True

Relax

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.

In [55]:
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.
In [44]:
### 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
Out[44]:
True

Check the energy difference here once again. Note how low it is compared to simply packing

delta = ?

In [50]:
### 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

Regional Relax

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.

In [52]:
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.

In [53]:
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.

In [54]:
### 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
Out[54]:
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!

Regional Relax - Cartesian

In [56]:
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?

In [57]:
### 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
Out[57]:
True

Regional Relax - Classic

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.

In [58]:
 
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
Out[58]:
True

How does the pose look? Better/worse than cartesian? No difference? How do the energies compare? Which is more general?

Conclusions

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!

In [ ]: