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

Working With Symmetry

Keywords: symmetry, asymmetric, SetupForSymmetryMover, virtual

Overview

Symmetry is an important concept to learn when working with biomolecules. When a protein is crystalized, it is in the precense of its symmetrical neighbors - which can be important if testing particular protocols or using crystal density for refinement or full structure building.

Symmetry can also be useful for designing symmetrical structures or large repeating meta-proteins like protein cages.

Symmetry In Rosetta

So why do we care if our protein is symmetrical or not when it comes to Rosetta? Each residue and atom that is loaded into Rosetta takes time to both load, and time to score. Since scoring can happen thousands of times - even in a short protocol, anything we can do to speed this up becomes important. The most expensive operation in Rosetta is minimization, and by using symmetry - we can reduce the minimization time exponentially by minimizing a single copy instead of ALL copies. We will get into the details about how this works below.

When we use symmetry in Rosetta - we are basically telling rosetta that the symmetrical partners are 'special', however, the total number of residues is now ALL residues, including symmetrical partners. Upon setting up symmety in Rosetta, Rosetta will replace the Conformation within the pose with a Symmetrical version, called the SymmetricConformation. If you know anything about classes, this SymmetricConformation is derived from the actual Conformation object, but contains extra information about the pose and some functions are replaced.

Symmetric Scoring and Moving

Ok, so now lets assume that we have our symmetric pose. Now what? Well, the symmetric copies are all tied to their real counterparts. Once you move a chain, residue, or atom by packing or minimization, the symmetric copies of that residue are all moved in the same way.

Cool. But what about scoring? Scoring works very similarly - instead of scoring each and every residue in our pose, Rosetta will score just our assymetric unit, and multiply that out to the number of symmetric copies we have. Intelligently, Rosetta will also figure out the symmetric interfaces that arise from the interactions of our assymetric unit to the symmetric copies and score them appropriately.

Symmetry-aware movers

Most of our common movers are symmetry-aware. At one point there were different symmetric and non-symmetric versions of particular code, such as MinMover and PackRotamersMover. Now though, Rosetta will automatically use the pose to figure out what needs to be done. You should seek original documentation (and contact the author if not explicit) to make sure that an uncommon protocol you are using is symmetry-aware.

Documentation

More information on RosettaSymmetry can be found in the following places:

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!")

Here, we will use a few specific options. The first three options make Rosetta a bit more robust to input structures. The -load_PDB_components cannot be used with glycans, unfortunately, and our structure has a few very important glycans. Finally, we load a bunch of glycan-specific options, which we will cover in the next tutorial.

In [1]:
from pyrosetta import *
from pyrosetta.rosetta import *
from pyrosetta.teaching import *
import os

init('-ignore_unrecognized_res -load_PDB_components false -ignore_zero_occupancy false @inputs/glycan_flags')
PyRosetta-4 2019 [Rosetta PyRosetta4.Release.python36.mac 2019.39+release.93456a567a8125cafdf7f8cb44400bc20b570d81 2019-09-26T14:24:44] retrieved from: http://www.pyrosetta.org
(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.
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.python36.mac r233 2019.39+release.93456a567a8 93456a567a8125cafdf7f8cb44400bc20b570d81 http://www.pyrosetta.org 2019-09-26T14:24:44
core.init: command: PyRosetta -ignore_unrecognized_res -load_PDB_components false -ignore_zero_occupancy false @inputs/glycan_flags -database /Users/jadolfbr/Library/Python/3.6/lib/python/site-packages/pyrosetta-2019.39+release.93456a567a8-py3.6-macosx-10.6-intel.egg/pyrosetta/database
basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1544006277 seed_offset=0 real_seed=1544006277
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1544006277 RG_type=mt19937

Creating a SymDef file

Here, we will start with how to create a basic symdef file for cyrstal symmetry. Note that there are ways to do this without a symdef file, but these do not currently work for glycan structures, which we will be using here.

The make_symdef_file.pl file is within Rosetta3. To use it, you will need to download and licence Rosetta3. The code is in the Rosetta/main/src/apps/public directory. In the interest of reducing code drift, this file is NOT included in the tutorial directory as we may then have version drift.

If you have done this, we can use the following command to create the symdef file. Here, the radius of symmetrical partners is 12A, which is certainly fairly large, but produces a very well represented crystal.

In [3]:
pdb = "inputs/1jnd.pdb"
base_cmd = f'cd inputs && make_symmdef_file.pl -r 12 -m CRYST -p  {pdb}.pdb > {pdb}_crys.symm && cd -'
print(base_cmd)
cd inputs && make_symmdef_file.pl -r 12 -m CRYST -p  inputs/1jnd.pdb.pdb > inputs/1jnd.pdb_crys.symm && cd -

Use this base command and the os.system(cmd) function to run the code or use the provided symdef file.

In [3]:
os.system('cp inputs/1jnd_crys.symm .')
Out[3]:
0

Take a look at the symmetrized structure in pymol (inputs/1jnd_symm.pdb). What would happen if we increased the radius to 24 instead of 12?

Setup a Symmetrized Pose

Here, we will run a basic Rosetta protocol with symmetry. There are much more complicated things you can do with symmetry, but for now, we just want to symmetrically pack the protein. Please see the docs for more on symmetry. The full Rosetta C++ tutorial for symmetry is a great place to go from here: - https://www.rosettacommons.org/demos/latest/tutorials/Symmetry/Symmetry

Lets first create a pose, and then use the SetupForSymmetryMover on the pose. Note this is an unrefined input structure. This is so that minmover will actually do something. A pareto-optimal refined structure can be found in the inputs as 1jnd_refined.pdb.gz

In [37]:
p = pose_from_pdb('inputs/1jnd.pdb')
original = p.clone()
core.import_pose.import_pose: File 'inputs/1jnd.pdb' automatically determined to be of type PDB
core.io.pdb.pdb_reader: Parsing 82 .pdb records with unknown format to search for Rosetta-specific comments.
core.io.util: Automatic glycan connection is activated.
core.io.util: Start reordering residues.
core.io.util: Corrected glycan residue order (internal numbering): [401, 402, 403, 404]
core.io.util: 
core.io.pose_from_sfr.PoseFromSFRBuilder: Setting chain termination for 404
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc401 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc402 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man403 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man404 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.
core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-beta-D-Glcp:2-AcNH 401.  Returning BOGUS ID instead.
core.conformation.Residue: [ WARNING ] missing an atom: 401  H1  that depends on a nonexistent polymer connection!
core.conformation.Residue: [ WARNING ]  --> generating it using idealized coordinates.
core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-beta-D-Glcp:2-AcNH 401.  Returning BOGUS ID instead.
core.conformation.Conformation: Found disulfide between residues 5 32
core.conformation.Conformation: current variant for 5 CYS
core.conformation.Conformation: current variant for 32 CYS
core.conformation.Conformation: current variant for 5 CYD
core.conformation.Conformation: current variant for 32 CYD
core.conformation.Conformation: Found disulfide between residues 302 385
core.conformation.Conformation: current variant for 302 CYS
core.conformation.Conformation: current variant for 385 CYS
core.conformation.Conformation: current variant for 302 CYD
core.conformation.Conformation: current variant for 385 CYD
core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees
core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.
In [38]:
p.total_residue()
Out[38]:
404
In [39]:
type(p.conformation())
Out[39]:
pyrosetta.rosetta.core.conformation.Conformation
In [40]:
symmetrize = rosetta.protocols.symmetry.SetupForSymmetryMover("1jnd_crys.symm")
symmetrize.apply(p)
core.conformation.symmetry.SymmData: [ WARNING ] Setting weight of master jump ( jump-id=1 ) to 1.0 (was undefined)
core.conformation.symmetry.SymmData: [ WARNING ] Setting jump_group JUMPGROUP1: [master 1]  6:0  7:0  2:0  3:0  4:0  5:0  8:0  9:0
core.conformation.symmetry.SymmData: [ WARNING ] Setting weight of master jump ( jump-id=10 ) to 1.0 (was undefined)
core.conformation.symmetry.SymmData: [ WARNING ] Setting jump_group JUMPGROUP2: [master 10]  20:0  22:0  12:0  14:0  16:0  18:0  24:0  26:0
core.conformation.symmetry.SymmData: symmetry name: 1jnd_P_32_2_1
core.conformation.symmetry.SymmData: number of subunits: 9
core.conformation.symmetry.SymmData: number of interfaces: 1
core.conformation.symmetry.SymmData: score subunit number: VRT_0_0_0_0
core.conformation.symmetry.SymmData: anchor the subunits at residue: 1
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_0_0_0_0
core.conformation.symmetry.SymmData: x: 1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: 73.8756 49.0221 11.025
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_0_0_0_0_base
core.conformation.symmetry.SymmData: x: 1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: 72.8756 48.0221 10.025
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_1_1_0_n1
core.conformation.symmetry.SymmData: x: -0.5 0.866025 0
core.conformation.symmetry.SymmData: y: -0.866025 -0.5 0
core.conformation.symmetry.SymmData: origin: 26.9528 39.4671 -18.9707
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_1_1_0_n1_base
core.conformation.symmetry.SymmData: x: -0.5 0.866025 0
core.conformation.symmetry.SymmData: y: -0.866025 -0.5 0
core.conformation.symmetry.SymmData: origin: 28.3188 39.1011 -19.9707
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_2_1_1_0
core.conformation.symmetry.SymmData: x: -0.5 -0.866025 0
core.conformation.symmetry.SymmData: y: 0.866025 -0.5 0
core.conformation.symmetry.SymmData: origin: 58.6891 3.60826 41.0206
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_2_1_1_0_base
core.conformation.symmetry.SymmData: x: -0.5 -0.866025 0
core.conformation.symmetry.SymmData: y: 0.866025 -0.5 0
core.conformation.symmetry.SymmData: origin: 58.3231 4.97428 40.0206
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_3_0_n1_0
core.conformation.symmetry.SymmData: x: -0.5 0.866025 0
core.conformation.symmetry.SymmData: y: 0.866025 0.5 0
core.conformation.symmetry.SymmData: origin: 58.6891 -3.60826 -11.025
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_3_0_n1_0_base
core.conformation.symmetry.SymmData: x: -0.5 0.866025 0
core.conformation.symmetry.SymmData: y: 0.866025 0.5 0
core.conformation.symmetry.SymmData: origin: 58.3231 -4.97428 -10.025
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_3_1_0_0
core.conformation.symmetry.SymmData: x: -0.5 0.866025 0
core.conformation.symmetry.SymmData: y: 0.866025 0.5 0
core.conformation.symmetry.SymmData: origin: 111.862 88.4892 -11.025
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_3_1_0_0_base
core.conformation.symmetry.SymmData: x: -0.5 0.866025 0
core.conformation.symmetry.SymmData: y: 0.866025 0.5 0
core.conformation.symmetry.SymmData: origin: 111.496 87.1232 -10.025
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_4_2_1_0
core.conformation.symmetry.SymmData: x: -0.5 -0.866025 0
core.conformation.symmetry.SymmData: y: -0.866025 0.5 0
core.conformation.symmetry.SymmData: origin: 80.1253 52.6304 48.9664
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_4_2_1_0_base
core.conformation.symmetry.SymmData: x: -0.5 -0.866025 0
core.conformation.symmetry.SymmData: y: -0.866025 0.5 0
core.conformation.symmetry.SymmData: origin: 81.4913 52.9964 49.9664
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_4_2_1_n1
core.conformation.symmetry.SymmData: x: -0.5 -0.866025 0
core.conformation.symmetry.SymmData: y: -0.866025 0.5 0
core.conformation.symmetry.SymmData: origin: 80.1253 52.6304 -41.0206
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_4_2_1_n1_base
core.conformation.symmetry.SymmData: x: -0.5 -0.866025 0
core.conformation.symmetry.SymmData: y: -0.866025 0.5 0
core.conformation.symmetry.SymmData: origin: 81.4913 52.9964 -40.0206
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_5_0_1_0
core.conformation.symmetry.SymmData: x: 1 0 0
core.conformation.symmetry.SymmData: y: -0 -1 0
core.conformation.symmetry.SymmData: origin: 20.7031 43.0754 18.9707
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_5_0_1_0_base
core.conformation.symmetry.SymmData: x: 1 0 0
core.conformation.symmetry.SymmData: y: -0 -1 0
core.conformation.symmetry.SymmData: origin: 19.7031 44.0754 19.9707
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_5_1_1_0
core.conformation.symmetry.SymmData: x: 1 0 0
core.conformation.symmetry.SymmData: y: -0 -1 0
core.conformation.symmetry.SymmData: origin: 127.048 43.0754 18.9707
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_5_1_1_0_base
core.conformation.symmetry.SymmData: x: 1 0 0
core.conformation.symmetry.SymmData: y: -0 -1 0
core.conformation.symmetry.SymmData: origin: 126.048 44.0754 19.9707
core.conformation.symmetry.SymmData: Dof for jump: 1
core.conformation.symmetry.SymmData: x 0:0,0:0,0 n2c
core.conformation.symmetry.SymmData: y 0:0,0:0,0 n2c
core.conformation.symmetry.SymmData: z 0:0,0:0,0 n2c
core.conformation.symmetry.SymmData: x_angle 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: y_angle 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: z_angle 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: Dof for jump: 10
core.conformation.symmetry.SymmData: x 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: y 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: z 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: x_angle 0:0,0:0,0 n2c
core.conformation.symmetry.SymmData: y_angle 0:0,0:0,0 n2c
core.conformation.symmetry.SymmData: z_angle 0:0,0:0,0 n2c
core.conformation.symmetry.SymmData: Jump JUMP_0_0_0_0_to_com VRT_0_0_0_0 VRT_0_0_0_0_base
core.conformation.symmetry.SymmData: Jump JUMP_0_0_0_0_to_subunit VRT_0_0_0_0_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_1_1_0_n1 VRT_0_0_0_0 VRT_1_1_0_n1
core.conformation.symmetry.SymmData: Jump JUMP_1_1_0_n1_to_com VRT_1_1_0_n1 VRT_1_1_0_n1_base
core.conformation.symmetry.SymmData: Jump JUMP_1_1_0_n1_to_subunit VRT_1_1_0_n1_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_2_1_1_0 VRT_0_0_0_0 VRT_2_1_1_0
core.conformation.symmetry.SymmData: Jump JUMP_2_1_1_0_to_com VRT_2_1_1_0 VRT_2_1_1_0_base
core.conformation.symmetry.SymmData: Jump JUMP_2_1_1_0_to_subunit VRT_2_1_1_0_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_3_0_n1_0 VRT_0_0_0_0 VRT_3_0_n1_0
core.conformation.symmetry.SymmData: Jump JUMP_3_0_n1_0_to_com VRT_3_0_n1_0 VRT_3_0_n1_0_base
core.conformation.symmetry.SymmData: Jump JUMP_3_0_n1_0_to_subunit VRT_3_0_n1_0_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_3_1_0_0 VRT_0_0_0_0 VRT_3_1_0_0
core.conformation.symmetry.SymmData: Jump JUMP_3_1_0_0_to_com VRT_3_1_0_0 VRT_3_1_0_0_base
core.conformation.symmetry.SymmData: Jump JUMP_3_1_0_0_to_subunit VRT_3_1_0_0_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_4_2_1_0 VRT_0_0_0_0 VRT_4_2_1_0
core.conformation.symmetry.SymmData: Jump JUMP_4_2_1_0_to_com VRT_4_2_1_0 VRT_4_2_1_0_base
core.conformation.symmetry.SymmData: Jump JUMP_4_2_1_0_to_subunit VRT_4_2_1_0_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_4_2_1_n1 VRT_0_0_0_0 VRT_4_2_1_n1
core.conformation.symmetry.SymmData: Jump JUMP_4_2_1_n1_to_com VRT_4_2_1_n1 VRT_4_2_1_n1_base
core.conformation.symmetry.SymmData: Jump JUMP_4_2_1_n1_to_subunit VRT_4_2_1_n1_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_5_0_1_0 VRT_0_0_0_0 VRT_5_0_1_0
core.conformation.symmetry.SymmData: Jump JUMP_5_0_1_0_to_com VRT_5_0_1_0 VRT_5_0_1_0_base
core.conformation.symmetry.SymmData: Jump JUMP_5_0_1_0_to_subunit VRT_5_0_1_0_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_5_1_1_0 VRT_0_0_0_0 VRT_5_1_1_0
core.conformation.symmetry.SymmData: Jump JUMP_5_1_1_0_to_com VRT_5_1_1_0 VRT_5_1_1_0_base
core.conformation.symmetry.SymmData: Jump JUMP_5_1_1_0_to_subunit VRT_5_1_1_0_base SUBUNIT
core.conformation.symmetry.SymmData: Include subunit:
core.conformation.symmetry.SymmData: Output subunit:
core.conformation.symmetry.SymmData: SlideType: RANDOM
core.conformation.symmetry.SymmData: SlideCriteriaType: CEN_DOCK_SCORE
core.conformation.symmetry.SymmData: SlideCriteriaVal: AUTOMATIC
core.conformation.symmetry.SymmData: SlideOrder: none
core.conformation.symmetry.util: =================== SYM FOLD TREE, jump notation: =symfixed= *indep* #symdof# jump[=follows] ========================
VRT_0_0_0_0(3637)
|----#j10#--->VRT_0_0_0_0_base(3638)----#j1#------>1:Sub1A(1-400)
|----=j11=--->VRT_1_1_0_n1(3643)---j12=10--->VRT_1_1_0_n1_base(3644)----j2=1---->1213:Sub4A(1213-1612)
|----=j13=--->VRT_2_1_1_0(3645)---j14=10--->VRT_2_1_1_0_base(3646)----j3=1---->1617:Sub5A(1617-2016)
|----=j15=--->VRT_3_0_n1_0(3647)---j16=10--->VRT_3_0_n1_0_base(3648)----j4=1---->2021:Sub6A(2021-2420)
|----=j17=--->VRT_3_1_0_0(3649)---j18=10--->VRT_3_1_0_0_base(3650)----j5=1---->2425:Sub7A(2425-2824)
|----=j19=--->VRT_4_2_1_0(3639)---j20=10--->VRT_4_2_1_0_base(3640)----j6=1---->405:Sub2A(405-804)
|----=j21=--->VRT_4_2_1_n1(3641)---j22=10--->VRT_4_2_1_n1_base(3642)----j7=1---->809:Sub3A(809-1208)
|----=j23=--->VRT_5_0_1_0(3651)---j24=10--->VRT_5_0_1_0_base(3652)----j8=1---->2829:Sub8A(2829-3228)
\----=j25=--->VRT_5_1_1_0(3653)---j26=10--->VRT_5_1_1_0_base(3654)----j9=1---->3233:Sub9A(3233-3632)
core.conformation.symmetry.Conformation: Found disulfide between residues 5 32
core.conformation.symmetry.Conformation: current variant for 5 CYD
core.conformation.symmetry.Conformation: current variant for 32 CYD
core.conformation.symmetry.Conformation: current variant for 5 CYD
core.conformation.symmetry.Conformation: current variant for 32 CYD
core.conformation.symmetry.Conformation: Add symmetric chemical bond 409 to 436
core.conformation.symmetry.Conformation: Add symmetric chemical bond 813 to 840
core.conformation.symmetry.Conformation: Add symmetric chemical bond 1217 to 1244
core.conformation.symmetry.Conformation: Add symmetric chemical bond 1621 to 1648
core.conformation.symmetry.Conformation: Add symmetric chemical bond 2025 to 2052
core.conformation.symmetry.Conformation: Add symmetric chemical bond 2429 to 2456
core.conformation.symmetry.Conformation: Add symmetric chemical bond 2833 to 2860
core.conformation.symmetry.Conformation: Add symmetric chemical bond 3237 to 3264
core.conformation.symmetry.Conformation: Add symmetric chemical bond 5 to 32
core.conformation.symmetry.Conformation: Found disulfide between residues 302 385
core.conformation.symmetry.Conformation: current variant for 302 CYD
core.conformation.symmetry.Conformation: current variant for 385 CYD
core.conformation.symmetry.Conformation: current variant for 302 CYD
core.conformation.symmetry.Conformation: current variant for 385 CYD
core.conformation.symmetry.Conformation: Add symmetric chemical bond 706 to 789
core.conformation.symmetry.Conformation: Add symmetric chemical bond 1110 to 1193
core.conformation.symmetry.Conformation: Add symmetric chemical bond 1514 to 1597
core.conformation.symmetry.Conformation: Add symmetric chemical bond 1918 to 2001
core.conformation.symmetry.Conformation: Add symmetric chemical bond 2322 to 2405
core.conformation.symmetry.Conformation: Add symmetric chemical bond 2726 to 2809
core.conformation.symmetry.Conformation: Add symmetric chemical bond 3130 to 3213
core.conformation.symmetry.Conformation: Add symmetric chemical bond 3534 to 3617
core.conformation.symmetry.Conformation: Add symmetric chemical bond 302 to 385
core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees
core.conformation.carbohydrates.GlycanTreeSet: Found 9 glycan trees.
protocols.simple_moves_symmetry.SymDockingInitialPerturbation: Reading options...
In [41]:
print(p.total_residue())
print(type(p.conformation()))
3654
<class 'pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation'>

How many symmetric copies do we have in our pose? How do the scores compare for our original pose and our symmetrized version?

Now lets use some of the functionality to understand how this all works. We can use the SymetricInfo object that is part of the SymmetricConformation to get at some info. Lets take a look at all residues and find the assymetric unit residues and equivalent residues for the rest.

In [42]:
print("AssymUnit? equivalent_res")
sym_info = p.conformation().Symmetry_Info()
for i in range(1, p.size()+1):
    print(i, sym_info.bb_is_independent(i), sym_info.bb_follows(i))
AssymUnit? equivalent_res
1 True 0
2 True 0
3 True 0
4 True 0
5 True 0
6 True 0
7 True 0
8 True 0
9 True 0
10 True 0
11 True 0
12 True 0
13 True 0
14 True 0
15 True 0
16 True 0
17 True 0
18 True 0
19 True 0
20 True 0
21 True 0
22 True 0
23 True 0
24 True 0
25 True 0
26 True 0
27 True 0
28 True 0
29 True 0
30 True 0
31 True 0
32 True 0
33 True 0
34 True 0
35 True 0
36 True 0
37 True 0
38 True 0
39 True 0
40 True 0
41 True 0
42 True 0
43 True 0
44 True 0
45 True 0
46 True 0
47 True 0
48 True 0
49 True 0
50 True 0
51 True 0
52 True 0
53 True 0
54 True 0
55 True 0
56 True 0
57 True 0
58 True 0
59 True 0
60 True 0
61 True 0
62 True 0
63 True 0
64 True 0
65 True 0
66 True 0
67 True 0
68 True 0
69 True 0
70 True 0
71 True 0
72 True 0
73 True 0
74 True 0
75 True 0
76 True 0
77 True 0
78 True 0
79 True 0
80 True 0
81 True 0
82 True 0
83 True 0
84 True 0
85 True 0
86 True 0
87 True 0
88 True 0
89 True 0
90 True 0
91 True 0
92 True 0
93 True 0
94 True 0
95 True 0
96 True 0
97 True 0
98 True 0
99 True 0
100 True 0
101 True 0
102 True 0
103 True 0
104 True 0
105 True 0
106 True 0
107 True 0
108 True 0
109 True 0
110 True 0
111 True 0
112 True 0
113 True 0
114 True 0
115 True 0
116 True 0
117 True 0
118 True 0
119 True 0
120 True 0
121 True 0
122 True 0
123 True 0
124 True 0
125 True 0
126 True 0
127 True 0
128 True 0
129 True 0
130 True 0
131 True 0
132 True 0
133 True 0
134 True 0
135 True 0
136 True 0
137 True 0
138 True 0
139 True 0
140 True 0
141 True 0
142 True 0
143 True 0
144 True 0
145 True 0
146 True 0
147 True 0
148 True 0
149 True 0
150 True 0
151 True 0
152 True 0
153 True 0
154 True 0
155 True 0
156 True 0
157 True 0
158 True 0
159 True 0
160 True 0
161 True 0
162 True 0
163 True 0
164 True 0
165 True 0
166 True 0
167 True 0
168 True 0
169 True 0
170 True 0
171 True 0
172 True 0
173 True 0
174 True 0
175 True 0
176 True 0
177 True 0
178 True 0
179 True 0
180 True 0
181 True 0
182 True 0
183 True 0
184 True 0
185 True 0
186 True 0
187 True 0
188 True 0
189 True 0
190 True 0
191 True 0
192 True 0
193 True 0
194 True 0
195 True 0
196 True 0
197 True 0
198 True 0
199 True 0
200 True 0
201 True 0
202 True 0
203 True 0
204 True 0
205 True 0
206 True 0
207 True 0
208 True 0
209 True 0
210 True 0
211 True 0
212 True 0
213 True 0
214 True 0
215 True 0
216 True 0
217 True 0
218 True 0
219 True 0
220 True 0
221 True 0
222 True 0
223 True 0
224 True 0
225 True 0
226 True 0
227 True 0
228 True 0
229 True 0
230 True 0
231 True 0
232 True 0
233 True 0
234 True 0
235 True 0
236 True 0
237 True 0
238 True 0
239 True 0
240 True 0
241 True 0
242 True 0
243 True 0
244 True 0
245 True 0
246 True 0
247 True 0
248 True 0
249 True 0
250 True 0
251 True 0
252 True 0
253 True 0
254 True 0
255 True 0
256 True 0
257 True 0
258 True 0
259 True 0
260 True 0
261 True 0
262 True 0
263 True 0
264 True 0
265 True 0
266 True 0
267 True 0
268 True 0
269 True 0
270 True 0
271 True 0
272 True 0
273 True 0
274 True 0
275 True 0
276 True 0
277 True 0
278 True 0
279 True 0
280 True 0
281 True 0
282 True 0
283 True 0
284 True 0
285 True 0
286 True 0
287 True 0
288 True 0
289 True 0
290 True 0
291 True 0
292 True 0
293 True 0
294 True 0
295 True 0
296 True 0
297 True 0
298 True 0
299 True 0
300 True 0
301 True 0
302 True 0
303 True 0
304 True 0
305 True 0
306 True 0
307 True 0
308 True 0
309 True 0
310 True 0
311 True 0
312 True 0
313 True 0
314 True 0
315 True 0
316 True 0
317 True 0
318 True 0
319 True 0
320 True 0
321 True 0
322 True 0
323 True 0
324 True 0
325 True 0
326 True 0
327 True 0
328 True 0
329 True 0
330 True 0
331 True 0
332 True 0
333 True 0
334 True 0
335 True 0
336 True 0
337 True 0
338 True 0
339 True 0
340 True 0
341 True 0
342 True 0
343 True 0
344 True 0
345 True 0
346 True 0
347 True 0
348 True 0
349 True 0
350 True 0
351 True 0
352 True 0
353 True 0
354 True 0
355 True 0
356 True 0
357 True 0
358 True 0
359 True 0
360 True 0
361 True 0
362 True 0
363 True 0
364 True 0
365 True 0
366 True 0
367 True 0
368 True 0
369 True 0
370 True 0
371 True 0
372 True 0
373 True 0
374 True 0
375 True 0
376 True 0
377 True 0
378 True 0
379 True 0
380 True 0
381 True 0
382 True 0
383 True 0
384 True 0
385 True 0
386 True 0
387 True 0
388 True 0
389 True 0
390 True 0
391 True 0
392 True 0
393 True 0
394 True 0
395 True 0
396 True 0
397 True 0
398 True 0
399 True 0
400 True 0
401 True 0
402 True 0
403 True 0
404 True 0
405 False 1
406 False 2
407 False 3
408 False 4
409 False 5
410 False 6
411 False 7
412 False 8
413 False 9
414 False 10
415 False 11
416 False 12
417 False 13
418 False 14
419 False 15
420 False 16
421 False 17
422 False 18
423 False 19
424 False 20
425 False 21
426 False 22
427 False 23
428 False 24
429 False 25
430 False 26
431 False 27
432 False 28
433 False 29
434 False 30
435 False 31
436 False 32
437 False 33
438 False 34
439 False 35
440 False 36
441 False 37
442 False 38
443 False 39
444 False 40
445 False 41
446 False 42
447 False 43
448 False 44
449 False 45
450 False 46
451 False 47
452 False 48
453 False 49
454 False 50
455 False 51
456 False 52
457 False 53
458 False 54
459 False 55
460 False 56
461 False 57
462 False 58
463 False 59
464 False 60
465 False 61
466 False 62
467 False 63
468 False 64
469 False 65
470 False 66
471 False 67
472 False 68
473 False 69
474 False 70
475 False 71
476 False 72
477 False 73
478 False 74
479 False 75
480 False 76
481 False 77
482 False 78
483 False 79
484 False 80
485 False 81
486 False 82
487 False 83
488 False 84
489 False 85
490 False 86
491 False 87
492 False 88
493 False 89
494 False 90
495 False 91
496 False 92
497 False 93
498 False 94
499 False 95
500 False 96
501 False 97
502 False 98
503 False 99
504 False 100
505 False 101
506 False 102
507 False 103
508 False 104
509 False 105
510 False 106
511 False 107
512 False 108
513 False 109
514 False 110
515 False 111
516 False 112
517 False 113
518 False 114
519 False 115
520 False 116
521 False 117
522 False 118
523 False 119
524 False 120
525 False 121
526 False 122
527 False 123
528 False 124
529 False 125
530 False 126
531 False 127
532 False 128
533 False 129
534 False 130
535 False 131
536 False 132
537 False 133
538 False 134
539 False 135
540 False 136
541 False 137
542 False 138
543 False 139
544 False 140
545 False 141
546 False 142
547 False 143
548 False 144
549 False 145
550 False 146
551 False 147
552 False 148
553 False 149
554 False 150
555 False 151
556 False 152
557 False 153
558 False 154
559 False 155
560 False 156
561 False 157
562 False 158
563 False 159
564 False 160
565 False 161
566 False 162
567 False 163
568 False 164
569 False 165
570 False 166
571 False 167
572 False 168
573 False 169
574 False 170
575 False 171
576 False 172
577 False 173
578 False 174
579 False 175
580 False 176
581 False 177
582 False 178
583 False 179
584 False 180
585 False 181
586 False 182
587 False 183
588 False 184
589 False 185
590 False 186
591 False 187
592 False 188
593 False 189
594 False 190
595 False 191
596 False 192
597 False 193
598 False 194
599 False 195
600 False 196
601 False 197
602 False 198
603 False 199
604 False 200
605 False 201
606 False 202
607 False 203
608 False 204
609 False 205
610 False 206
611 False 207
612 False 208
613 False 209
614 False 210
615 False 211
616 False 212
617 False 213
618 False 214
619 False 215
620 False 216
621 False 217
622 False 218
623 False 219
624 False 220
625 False 221
626 False 222
627 False 223
628 False 224
629 False 225
630 False 226
631 False 227
632 False 228
633 False 229
634 False 230
635 False 231
636 False 232
637 False 233
638 False 234
639 False 235
640 False 236
641 False 237
642 False 238
643 False 239
644 False 240
645 False 241
646 False 242
647 False 243
648 False 244
649 False 245
650 False 246
651 False 247
652 False 248
653 False 249
654 False 250
655 False 251
656 False 252
657 False 253
658 False 254
659 False 255
660 False 256
661 False 257
662 False 258
663 False 259
664 False 260
665 False 261
666 False 262
667 False 263
668 False 264
669 False 265
670 False 266
671 False 267
672 False 268
673 False 269
674 False 270
675 False 271
676 False 272
677 False 273
678 False 274
679 False 275
680 False 276
681 False 277
682 False 278
683 False 279
684 False 280
685 False 281
686 False 282
687 False 283
688 False 284
689 False 285
690 False 286
691 False 287
692 False 288
693 False 289
694 False 290
695 False 291
696 False 292
697 False 293
698 False 294
699 False 295
700 False 296
701 False 297
702 False 298
703 False 299
704 False 300
705 False 301
706 False 302
707 False 303
708 False 304
709 False 305
710 False 306
711 False 307
712 False 308
713 False 309
714 False 310
715 False 311
716 False 312
717 False 313
718 False 314
719 False 315
720 False 316
721 False 317
722 False 318
723 False 319
724 False 320
725 False 321
726 False 322
727 False 323
728 False 324
729 False 325
730 False 326
731 False 327
732 False 328
733 False 329
734 False 330
735 False 331
736 False 332
737 False 333
738 False 334
739 False 335
740 False 336
741 False 337
742 False 338
743 False 339
744 False 340
745 False 341
746 False 342
747 False 343
748 False 344
749 False 345
750 False 346
751 False 347
752 False 348
753 False 349
754 False 350
755 False 351
756 False 352
757 False 353
758 False 354
759 False 355
760 False 356
761 False 357
762 False 358
763 False 359
764 False 360
765 False 361
766 False 362
767 False 363
768 False 364
769 False 365
770 False 366
771 False 367
772 False 368
773 False 369
774 False 370
775 False 371
776 False 372
777 False 373
778 False 374
779 False 375
780 False 376
781 False 377
782 False 378
783 False 379
784 False 380
785 False 381
786 False 382
787 False 383
788 False 384
789 False 385
790 False 386
791 False 387
792 False 388
793 False 389
794 False 390
795 False 391
796 False 392
797 False 393
798 False 394
799 False 395
800 False 396
801 False 397
802 False 398
803 False 399
804 False 400
805 False 401
806 False 402
807 False 403
808 False 404
809 False 1
810 False 2
811 False 3
812 False 4
813 False 5
814 False 6
815 False 7
816 False 8
817 False 9
818 False 10
819 False 11
820 False 12
821 False 13
822 False 14
823 False 15
824 False 16
825 False 17
826 False 18
827 False 19
828 False 20
829 False 21
830 False 22
831 False 23
832 False 24
833 False 25
834 False 26
835 False 27
836 False 28
837 False 29
838 False 30
839 False 31
840 False 32
841 False 33
842 False 34
843 False 35
844 False 36
845 False 37
846 False 38
847 False 39
848 False 40
849 False 41
850 False 42
851 False 43
852 False 44
853 False 45
854 False 46
855 False 47
856 False 48
857 False 49
858 False 50
859 False 51
860 False 52
861 False 53
862 False 54
863 False 55
864 False 56
865 False 57
866 False 58
867 False 59
868 False 60
869 False 61
870 False 62
871 False 63
872 False 64
873 False 65
874 False 66
875 False 67
876 False 68
877 False 69
878 False 70
879 False 71
880 False 72
881 False 73
882 False 74
883 False 75
884 False 76
885 False 77
886 False 78
887 False 79
888 False 80
889 False 81
890 False 82
891 False 83
892 False 84
893 False 85
894 False 86
895 False 87
896 False 88
897 False 89
898 False 90
899 False 91
900 False 92
901 False 93
902 False 94
903 False 95
904 False 96
905 False 97
906 False 98
907 False 99
908 False 100
909 False 101
910 False 102
911 False 103
912 False 104
913 False 105
914 False 106
915 False 107
916 False 108
917 False 109
918 False 110
919 False 111
920 False 112
921 False 113
922 False 114
923 False 115
924 False 116
925 False 117
926 False 118
927 False 119
928 False 120
929 False 121
930 False 122
931 False 123
932 False 124
933 False 125
934 False 126
935 False 127
936 False 128
937 False 129
938 False 130
939 False 131
940 False 132
941 False 133
942 False 134
943 False 135
944 False 136
945 False 137
946 False 138
947 False 139
948 False 140
949 False 141
950 False 142
951 False 143
952 False 144
953 False 145
954 False 146
955 False 147
956 False 148
957 False 149
958 False 150
959 False 151
960 False 152
961 False 153
962 False 154
963 False 155
964 False 156
965 False 157
966 False 158
967 False 159
968 False 160
969 False 161
970 False 162
971 False 163
972 False 164
973 False 165
974 False 166
975 False 167
976 False 168
977 False 169
978 False 170
979 False 171
980 False 172
981 False 173
982 False 174
983 False 175
984 False 176
985 False 177
986 False 178
987 False 179
988 False 180
989 False 181
990 False 182
991 False 183
992 False 184
993 False 185
994 False 186
995 False 187
996 False 188
997 False 189
998 False 190
999 False 191
1000 False 192
1001 False 193
1002 False 194
1003 False 195
1004 False 196
1005 False 197
1006 False 198
1007 False 199
1008 False 200
1009 False 201
1010 False 202
1011 False 203
1012 False 204
1013 False 205
1014 False 206
1015 False 207
1016 False 208
1017 False 209
1018 False 210
1019 False 211
1020 False 212
1021 False 213
1022 False 214
1023 False 215
1024 False 216
1025 False 217
1026 False 218
1027 False 219
1028 False 220
1029 False 221
1030 False 222
1031 False 223
1032 False 224
1033 False 225
1034 False 226
1035 False 227
1036 False 228
1037 False 229
1038 False 230
1039 False 231
1040 False 232
1041 False 233
1042 False 234
1043 False 235
1044 False 236
1045 False 237
1046 False 238
1047 False 239
1048 False 240
1049 False 241
1050 False 242
1051 False 243
1052 False 244
1053 False 245
1054 False 246
1055 False 247
1056 False 248
1057 False 249
1058 False 250
1059 False 251
1060 False 252
1061 False 253
1062 False 254
1063 False 255
1064 False 256
1065 False 257
1066 False 258
1067 False 259
1068 False 260
1069 False 261
1070 False 262
1071 False 263
1072 False 264
1073 False 265
1074 False 266
1075 False 267
1076 False 268
1077 False 269
1078 False 270
1079 False 271
1080 False 272
1081 False 273
1082 False 274
1083 False 275
1084 False 276
1085 False 277
1086 False 278
1087 False 279
1088 False 280
1089 False 281
1090 False 282
1091 False 283
1092 False 284
1093 False 285
1094 False 286
1095 False 287
1096 False 288
1097 False 289
1098 False 290
1099 False 291
1100 False 292
1101 False 293
1102 False 294
1103 False 295
1104 False 296
1105 False 297
1106 False 298
1107 False 299
1108 False 300
1109 False 301
1110 False 302
1111 False 303
1112 False 304
1113 False 305
1114 False 306
1115 False 307
1116 False 308
1117 False 309
1118 False 310
1119 False 311
1120 False 312
1121 False 313
1122 False 314
1123 False 315
1124 False 316
1125 False 317
1126 False 318
1127 False 319
1128 False 320
1129 False 321
1130 False 322
1131 False 323
1132 False 324
1133 False 325
1134 False 326
1135 False 327
1136 False 328
1137 False 329
1138 False 330
1139 False 331
1140 False 332
1141 False 333
1142 False 334
1143 False 335
1144 False 336
1145 False 337
1146 False 338
1147 False 339
1148 False 340
1149 False 341
1150 False 342
1151 False 343
1152 False 344
1153 False 345
1154 False 346
1155 False 347
1156 False 348
1157 False 349
1158 False 350
1159 False 351
1160 False 352
1161 False 353
1162 False 354
1163 False 355
1164 False 356
1165 False 357
1166 False 358
1167 False 359
1168 False 360
1169 False 361
1170 False 362
1171 False 363
1172 False 364
1173 False 365
1174 False 366
1175 False 367
1176 False 368
1177 False 369
1178 False 370
1179 False 371
1180 False 372
1181 False 373
1182 False 374
1183 False 375
1184 False 376
1185 False 377
1186 False 378
1187 False 379
1188 False 380
1189 False 381
1190 False 382
1191 False 383
1192 False 384
1193 False 385
1194 False 386
1195 False 387
1196 False 388
1197 False 389
1198 False 390
1199 False 391
1200 False 392
1201 False 393
1202 False 394
1203 False 395
1204 False 396
1205 False 397
1206 False 398
1207 False 399
1208 False 400
1209 False 401
1210 False 402
1211 False 403
1212 False 404
1213 False 1
1214 False 2
1215 False 3
1216 False 4
1217 False 5
1218 False 6
1219 False 7
1220 False 8
1221 False 9
1222 False 10
1223 False 11
1224 False 12
1225 False 13
1226 False 14
1227 False 15
1228 False 16
1229 False 17
1230 False 18
1231 False 19
1232 False 20
1233 False 21
1234 False 22
1235 False 23
1236 False 24
1237 False 25
1238 False 26
1239 False 27
1240 False 28
1241 False 29
1242 False 30
1243 False 31
1244 False 32
1245 False 33
1246 False 34
1247 False 35
1248 False 36
1249 False 37
1250 False 38
1251 False 39
1252 False 40
1253 False 41
1254 False 42
1255 False 43
1256 False 44
1257 False 45
1258 False 46
1259 False 47
1260 False 48
1261 False 49
1262 False 50
1263 False 51
1264 False 52
1265 False 53
1266 False 54
1267 False 55
1268 False 56
1269 False 57
1270 False 58
1271 False 59
1272 False 60
1273 False 61
1274 False 62
1275 False 63
1276 False 64
1277 False 65
1278 False 66
1279 False 67
1280 False 68
1281 False 69
1282 False 70
1283 False 71
1284 False 72
1285 False 73
1286 False 74
1287 False 75
1288 False 76
1289 False 77
1290 False 78
1291 False 79
1292 False 80
1293 False 81
1294 False 82
1295 False 83
1296 False 84
1297 False 85
1298 False 86
1299 False 87
1300 False 88
1301 False 89
1302 False 90
1303 False 91
1304 False 92
1305 False 93
1306 False 94
1307 False 95
1308 False 96
1309 False 97
1310 False 98
1311 False 99
1312 False 100
1313 False 101
1314 False 102
1315 False 103
1316 False 104
1317 False 105
1318 False 106
1319 False 107
1320 False 108
1321 False 109
1322 False 110
1323 False 111
1324 False 112
1325 False 113
1326 False 114
1327 False 115
1328 False 116
1329 False 117
1330 False 118
1331 False 119
1332 False 120
1333 False 121
1334 False 122
1335 False 123
1336 False 124
1337 False 125
1338 False 126
1339 False 127
1340 False 128
1341 False 129
1342 False 130
1343 False 131
1344 False 132
1345 False 133
1346 False 134
1347 False 135
1348 False 136
1349 False 137
1350 False 138
1351 False 139
1352 False 140
1353 False 141
1354 False 142
1355 False 143
1356 False 144
1357 False 145
1358 False 146
1359 False 147
1360 False 148
1361 False 149
1362 False 150
1363 False 151
1364 False 152
1365 False 153
1366 False 154
1367 False 155
1368 False 156
1369 False 157
1370 False 158
1371 False 159
1372 False 160
1373 False 161
1374 False 162
1375 False 163
1376 False 164
1377 False 165
1378 False 166
1379 False 167
1380 False 168
1381 False 169
1382 False 170
1383 False 171
1384 False 172
1385 False 173
1386 False 174
1387 False 175
1388 False 176
1389 False 177
1390 False 178
1391 False 179
1392 False 180
1393 False 181
1394 False 182
1395 False 183
1396 False 184
1397 False 185
1398 False 186
1399 False 187
1400 False 188
1401 False 189
1402 False 190
1403 False 191
1404 False 192
1405 False 193
1406 False 194
1407 False 195
1408 False 196
1409 False 197
1410 False 198
1411 False 199
1412 False 200
1413 False 201
1414 False 202
1415 False 203
1416 False 204
1417 False 205
1418 False 206
1419 False 207
1420 False 208
1421 False 209
1422 False 210
1423 False 211
1424 False 212
1425 False 213
1426 False 214
1427 False 215
1428 False 216
1429 False 217
1430 False 218
1431 False 219
1432 False 220
1433 False 221
1434 False 222
1435 False 223
1436 False 224
1437 False 225
1438 False 226
1439 False 227
1440 False 228
1441 False 229
1442 False 230
1443 False 231
1444 False 232
1445 False 233
1446 False 234
1447 False 235
1448 False 236
1449 False 237
1450 False 238
1451 False 239
1452 False 240
1453 False 241
1454 False 242
1455 False 243
1456 False 244
1457 False 245
1458 False 246
1459 False 247
1460 False 248
1461 False 249
1462 False 250
1463 False 251
1464 False 252
1465 False 253
1466 False 254
1467 False 255
1468 False 256
1469 False 257
1470 False 258
1471 False 259
1472 False 260
1473 False 261
1474 False 262
1475 False 263
1476 False 264
1477 False 265
1478 False 266
1479 False 267
1480 False 268
1481 False 269
1482 False 270
1483 False 271
1484 False 272
1485 False 273
1486 False 274
1487 False 275
1488 False 276
1489 False 277
1490 False 278
1491 False 279
1492 False 280
1493 False 281
1494 False 282
1495 False 283
1496 False 284
1497 False 285
1498 False 286
1499 False 287
1500 False 288
1501 False 289
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3637 True 0
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3640 True 0
3641 True 0
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3644 True 0
3645 True 0
3646 True 0
3647 True 0
3648 True 0
3649 True 0
3650 True 0
3651 True 0
3652 True 0
3653 True 0
3654 True 0

Which residues are our original pose residues? Note that the final residues are called Virtual residues. Virtual residues are not scored. They have coordinates, and can move, but simply result in a score of zero. They are useful in some contexts to hide a part of the pose from the scoring machinery, and there are movers that can change residues to and from virtual. In this case, they are used for the FoldTree - in order to allow refinement of the full crystal environment. They allow relative movement of each subunit relative to each other. There are two virtual residues for each subunit

In [43]:
print(p.residue(3654))
Residue 3654: VRT (XXX, X):
Base: VRT
 Properties: LIGAND VIRTUAL_RESIDUE
 Variant types:
 Main-chain atoms:
 Backbone atoms:  
 Side-chain atoms: ORIG  X    Y  
Atom Coordinates:
  ORIG: 126.048, 44.0754, 19.9707 (virtual)
   X  : 127.048, 44.0754, 19.9707 (virtual)
   Y  : 126.048, 43.0754, 19.9707 (virtual)
Mirrored relative to coordinates in ResidueType: FALSE

In [44]:
print("Total Subunits:", (3654-18)/404)
print("Total Subunits:", sym_info.subunits())
Total Subunits: 9.0
Total Subunits: 9
In [45]:
score = get_score_function()
print(score(original))
print(score(p))
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: The -include_sugars flag was used with no sugar_bb weight set in the weights file.  Setting sugar_bb weight to 1.0 by default.
-531.2534669946483
-1132.7274634504747

Running Protocols with Symmetry

Now, lets try running a minimization with symmetry on.

In [54]:
mm = MoveMap()
mm.set_bb(True)
mm.set_chi(True)
minmover = rosetta.protocols.minimization_packing.MinMover()
minmover.score_function(score)
minmover.set_movemap(mm)
if not os.getenv("DEBUG"):
    minmover.apply(p)
In [55]:
score(p)
Out[55]:
-1147.371462425749

How does our pose look? For being such a large pose, how was the speed of minimization?

How does this compare to our refined pose? Try to copy a subunit to a new object in PyMol. Then use the align command to align it to our assymetric unit. What is the RMSD?

Now lets pack with our symmetric structure.

In [68]:
from rosetta.core.pack.task import *
from rosetta.core.pack.task.operation import *

packer = PackRotamersMover()
tf = rosetta.core.pack.task.TaskFactory()

tf.push_back(RestrictToRepacking())
tf.push_back(IncludeCurrent())
packer.task_factory(tf)

p = original.clone()
symmetrize.apply(p)
core.conformation.symmetry.util: =================== SYM FOLD TREE, jump notation: =symfixed= *indep* #symdof# jump[=follows] ========================
VRT_0_0_0_0(3637)
|----#j10#--->VRT_0_0_0_0_base(3638)----#j1#------>1:Sub1A(1-400)
|----=j11=--->VRT_1_1_0_n1(3643)---j12=10--->VRT_1_1_0_n1_base(3644)----j2=1---->1213:Sub4A(1213-1612)
|----=j13=--->VRT_2_1_1_0(3645)---j14=10--->VRT_2_1_1_0_base(3646)----j3=1---->1617:Sub5A(1617-2016)
|----=j15=--->VRT_3_0_n1_0(3647)---j16=10--->VRT_3_0_n1_0_base(3648)----j4=1---->2021:Sub6A(2021-2420)
|----=j17=--->VRT_3_1_0_0(3649)---j18=10--->VRT_3_1_0_0_base(3650)----j5=1---->2425:Sub7A(2425-2824)
|----=j19=--->VRT_4_2_1_0(3639)---j20=10--->VRT_4_2_1_0_base(3640)----j6=1---->405:Sub2A(405-804)
|----=j21=--->VRT_4_2_1_n1(3641)---j22=10--->VRT_4_2_1_n1_base(3642)----j7=1---->809:Sub3A(809-1208)
|----=j23=--->VRT_5_0_1_0(3651)---j24=10--->VRT_5_0_1_0_base(3652)----j8=1---->2829:Sub8A(2829-3228)
\----=j25=--->VRT_5_1_1_0(3653)---j26=10--->VRT_5_1_1_0_base(3654)----j9=1---->3233:Sub9A(3233-3632)
core.conformation.symmetry.Conformation: Found disulfide between residues 5 32
core.conformation.symmetry.Conformation: current variant for 5 CYD
core.conformation.symmetry.Conformation: current variant for 32 CYD
core.conformation.symmetry.Conformation: current variant for 5 CYD
core.conformation.symmetry.Conformation: current variant for 32 CYD
core.conformation.symmetry.Conformation: Add symmetric chemical bond 409 to 436
core.conformation.symmetry.Conformation: Add symmetric chemical bond 813 to 840
core.conformation.symmetry.Conformation: Add symmetric chemical bond 1217 to 1244
core.conformation.symmetry.Conformation: Add symmetric chemical bond 1621 to 1648
core.conformation.symmetry.Conformation: Add symmetric chemical bond 2025 to 2052
core.conformation.symmetry.Conformation: Add symmetric chemical bond 2429 to 2456
core.conformation.symmetry.Conformation: Add symmetric chemical bond 2833 to 2860
core.conformation.symmetry.Conformation: Add symmetric chemical bond 3237 to 3264
core.conformation.symmetry.Conformation: Add symmetric chemical bond 5 to 32
core.conformation.symmetry.Conformation: Found disulfide between residues 302 385
core.conformation.symmetry.Conformation: current variant for 302 CYD
core.conformation.symmetry.Conformation: current variant for 385 CYD
core.conformation.symmetry.Conformation: current variant for 302 CYD
core.conformation.symmetry.Conformation: current variant for 385 CYD
core.conformation.symmetry.Conformation: Add symmetric chemical bond 706 to 789
core.conformation.symmetry.Conformation: Add symmetric chemical bond 1110 to 1193
core.conformation.symmetry.Conformation: Add symmetric chemical bond 1514 to 1597
core.conformation.symmetry.Conformation: Add symmetric chemical bond 1918 to 2001
core.conformation.symmetry.Conformation: Add symmetric chemical bond 2322 to 2405
core.conformation.symmetry.Conformation: Add symmetric chemical bond 2726 to 2809
core.conformation.symmetry.Conformation: Add symmetric chemical bond 3130 to 3213
core.conformation.symmetry.Conformation: Add symmetric chemical bond 3534 to 3617
core.conformation.symmetry.Conformation: Add symmetric chemical bond 302 to 385
core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees
core.conformation.carbohydrates.GlycanTreeSet: Found 9 glycan trees.
protocols.simple_moves_symmetry.SymDockingInitialPerturbation: Reading options...
In [69]:
if not os.getenv("DEBUG"):
    packer.apply(p)
protocols.minimization_packing.PackRotamersMover: [ WARNING ] undefined ScoreFunction -- creating a default one
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: The -include_sugars flag was used with no sugar_bb weight set in the weights file.  Setting sugar_bb weight to 1.0 by default.
core.pack.rotamer_set.RotamerSet_: [ WARNING ] including current in order to get at least 1 rotamer !!!!!! 180 ASN:N-glycosylated
core.pack.pack_rotamers: built 5259 rotamers at 404 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
In [70]:
print("packed", score(p))
packed -1960.9189300248413

Conclusions

Symmetry is a useful tool in the Rosetta Library. There are also selectors and movers that you may find useful, such as the AsymmetricUnitSelector in rosetta.core.select.residue_selectors and the ExtractAsymmetricUnitMover, which will give you back just the single subunit, without any asymetric partners, and the ExtractAsymmetricPoseMover, which will remove 'symmetry' information and give you back a pose with all the subunits. The later of these can be found by importing rosetta.protocols.symmetry.

Note that not ALL protocols will respect symmetry - so please check the original documentation to see if symmetry is supported. If you are unsure, please email the developer.

In [ ]:
 

Chapter contributors:

  • Jared Adolf-Bryfogle (Scripps; Institute for Protein Innovation)