Positive scores with SymmDock in helical symmetry

[Anonymous]

Keywords:
SymmDock
Helical Symmetry

Hi, again.
Now I am trying to rebuild an actin filament(PDB ID: 3g37) with helical symmetry by using the symmdock protocol, in order to test and get familiar with the protocol.
Before using Symmdock, I relaxed the subunit with sidechain constraint and got ~-300 REU, which seemed a little high and might be caused by the low-resolution of 3g37, because there are 375 residues per subunit.
Then I used the SymmDock to rebuild the filament model, with sdf generated by make_symmdef_file.pl.
Despite of the output model having the same helical symmetry (rmsd vs 3g37 < 0.3) , the total_score is positive. So I wonder if the high score was just caused by backbone positional errors of the subunit because the total_score of the subunit seemed a little unreasonable as mentioned above, or positive scores are also reasonable for symmdock protocol? ==================================================================================================
The total_score, I_sc, fa_rep, fa_sol are positive.
Here are the scores:
SCORE: total_score I_sc dslf_ca_dih dslf_cs_ang dslf_ss_dih dslf_ss_dst fa_atr fa_dun fa_elec fa_pair fa_rep fa_sol hbond_bb_sc hbond_lr_bb hbond_sc hbond_sr_bb description
SCORE: 352.747 6560.169 0.000 0.000 0.000 0.000 -548.148 23.655 -3.499 -8.872 681.072 240.634 -4.183 -7.237 -6.660 -14.016 3g37sub_0001

And here are the sdf:

symmetry_name 3g37_helix_C1
E = 1*VRT_0_0_0_base + 1*(VRT_0_0_0_base:VRT_0_1_0_base)
anchor_residue COM
virtual_coordinates_start
xyz VRT_0 1.000000,0.000000,0.000000 0.000000,1.000000,0.000000 136.384157,136.226571,268.007075
xyz VRT_0_n4_0 0.176174,0.984358,0.001135 -0.984359,0.176173,0.000527 136.418955,136.094439,377.152985
xyz VRT_0_n4_0_base 0.176174,0.984358,0.001135 -0.984359,0.176173,0.000527 133.776623,121.330597,377.135955
xyz VRT_0_n3_0 -0.395324,-0.918541,-0.000986 0.918542,-0.395323,-0.000771 136.410256,136.127472,349.866508
xyz VRT_0_n3_0_base -0.395324,-0.918541,-0.000986 0.918542,-0.395323,-0.000771 142.339498,149.904159,349.881295
xyz VRT_0_n2_0 0.593775,0.804630,0.000785 -0.804631,0.593775,0.000975 136.401556,136.160505,322.580030
xyz VRT_0_n2_0_base 0.593775,0.804630,0.000785 -0.804631,0.593775,0.000975 127.495851,124.092303,322.568260
xyz VRT_0_n1_0 -0.761138,-0.648590,-0.000543 0.648590,-0.761137,-0.001128 136.392856,136.193538,295.293552
xyz VRT_0_n1_0_base -0.761138,-0.648590,-0.000543 0.648590,-0.761137,-0.001128 147.808733,145.921381,295.301689
xyz VRT_0_0_0 0.888648,0.458591,0.000272 -0.458591,0.888647,0.001222 136.384157,136.226571,268.007075
xyz VRT_0_0_0_base 0.888648,0.458591,0.000272 -0.458591,0.888647,0.001222 123.055829,129.348425,268.002997
xyz VRT_0_1_0 -0.969629,-0.244580,0.000013 0.244580,-0.969628,-0.001252 136.375457,136.259604,240.720597
xyz VRT_0_1_0_base -0.969629,-0.244580,0.000013 0.244580,-0.969628,-0.001252 150.918382,139.927922,240.720401
xyz VRT_0_2_0 0.999842,0.017763,-0.000297 -0.017763,0.999841,0.001216 136.366757,136.292637,213.434119
xyz VRT_0_2_0_base 0.999842,0.017763,-0.000297 -0.017763,0.999841,0.001216 121.370684,136.026215,213.438578
xyz VRT_0_3_0 -0.977705,0.209983,0.000566 -0.209984,-0.977704,-0.001117 136.358058,136.325670,186.147641
xyz VRT_0_3_0_base -0.977705,0.209983,0.000566 -0.209984,-0.977704,-0.001117 151.022106,133.176247,186.139153
xyz VRT_0_4_0 0.904376,-0.426736,-0.000805 0.426736,0.904376,0.000959 136.349358,136.358703,158.861164
xyz VRT_0_4_0_base 0.904376,-0.426736,-0.000805 0.426736,0.904376,0.000959 122.785127,142.759072,158.873237
virtual_coordinates_stop
connect_virtual JUMP_0 VRT_0 VRT_0_n4_0
connect_virtual JUMP_0_n4_0 VRT_0_n4_0 VRT_0_n3_0
connect_virtual JUMP_0_n3_0 VRT_0_n3_0 VRT_0_n2_0
connect_virtual JUMP_0_n2_0 VRT_0_n2_0 VRT_0_n1_0
connect_virtual JUMP_0_n1_0 VRT_0_n1_0 VRT_0_0_0
connect_virtual JUMP_0_0_0 VRT_0_0_0 VRT_0_1_0
connect_virtual JUMP_0_1_0 VRT_0_1_0 VRT_0_2_0
connect_virtual JUMP_0_2_0 VRT_0_2_0 VRT_0_3_0
connect_virtual JUMP_0_3_0 VRT_0_3_0 VRT_0_4_0
connect_virtual JUMP_0_n4_0_to_com VRT_0_n4_0 VRT_0_n4_0_base
connect_virtual JUMP_0_n3_0_to_com VRT_0_n3_0 VRT_0_n3_0_base
connect_virtual JUMP_0_n2_0_to_com VRT_0_n2_0 VRT_0_n2_0_base
connect_virtual JUMP_0_n1_0_to_com VRT_0_n1_0 VRT_0_n1_0_base
connect_virtual JUMP_0_0_0_to_com VRT_0_0_0 VRT_0_0_0_base
connect_virtual JUMP_0_1_0_to_com VRT_0_1_0 VRT_0_1_0_base
connect_virtual JUMP_0_2_0_to_com VRT_0_2_0 VRT_0_2_0_base
connect_virtual JUMP_0_3_0_to_com VRT_0_3_0 VRT_0_3_0_base
connect_virtual JUMP_0_4_0_to_com VRT_0_4_0 VRT_0_4_0_base
connect_virtual JUMP_0_n4_0_to_subunit VRT_0_n4_0_base SUBUNIT
connect_virtual JUMP_0_n3_0_to_subunit VRT_0_n3_0_base SUBUNIT
connect_virtual JUMP_0_n2_0_to_subunit VRT_0_n2_0_base SUBUNIT
connect_virtual JUMP_0_n1_0_to_subunit VRT_0_n1_0_base SUBUNIT
connect_virtual JUMP_0_0_0_to_subunit VRT_0_0_0_base SUBUNIT
connect_virtual JUMP_0_1_0_to_subunit VRT_0_1_0_base SUBUNIT
connect_virtual JUMP_0_2_0_to_subunit VRT_0_2_0_base SUBUNIT
connect_virtual JUMP_0_3_0_to_subunit VRT_0_3_0_base SUBUNIT
connect_virtual JUMP_0_4_0_to_subunit VRT_0_4_0_base SUBUNIT
set_dof JUMP_0_0_0 z(27.25958893) angle_z
set_dof JUMP_0_0_0_to_com x(15.1065021)
set_dof JUMP_0_0_0_to_subunit angle_x angle_y angle_z
set_jump_group JUMPGROUP1 JUMP_0_0_0:1 JUMP_0_1_0:2 JUMP_0_n1_0 JUMP_0_2_0:3 JUMP_0_n2_0 JUMP_0_3_0:4 JUMP_0_n3_0 JUMP_0_n4_0
set_jump_group JUMPGROUP2 JUMP_0_0_0_to_com JUMP_0_1_0_to_com JUMP_0_n1_0_to_com JUMP_0_2_0_to_com JUMP_0_n2_0_to_com JUMP_0_3_0_to_com JUMP_0_n3_0_to_com JUMP_0_4_0_to_com JUMP_0_n4_0_to_com
set_jump_group JUMPGROUP3 JUMP_0_0_0_to_subunit JUMP_0_1_0_to_subunit JUMP_0_n1_0_to_subunit JUMP_0_2_0_to_subunit JUMP_0_n2_0_to_subunit JUMP_0_3_0_to_subunit JUMP_0_n3_0_to_subunit JUMP_0_4_0_to_subunit JUMP_0_n4_0_to_subunit

Here are the flags:
-in:file:s 3g37sub.pdb
-database /home/rosetta_2013wk40_bundle/main/database
-symmetry:symmetry_definition 3g37.symm3

-packing:ex1
-packing:ex2aro
-out:nstruct 1000
-out:file:fullatom
-symmetry:initialize_rigid_body_dofs
-docking:docking_local_refine
-docking:dock_ppk
-symmetry:symmetric_rmsd

Thank you already in advance!

[Anonymous]

Also, I am confused about the set_dof statements.
For example, set_dof JUMP_0_0_0_to_com x(15.1065021)
I know that the jump is initialized along the x direction with a value of 15.1065021, but will the translation along x axis keep the same in the “slide into contact” steps? Or the translation value of 15.1065021 is just an initial value and will be changed in the following steps?

[Anonymous]

In looking for why your protein is high scoring, I’d recommend looking at the per residue scores. These should be output in the bottom of the PDB file. If the high energy is confined to a certain region or set of residues, it’ll be listed there.

To troubleshoot whether it’s a symdef file problem, you may want to rescore your complex with all the symmetric partners present, but without symmetry.

Finally, you may want to use the residue_energy_breakdown application (available in the weeklies) to see which residue pairs are contributing the high energy. I don’t know if that application is symmetry-aware, though, so you may have to score as a non-symmetric complete complex.

[Anonymous]

Thank you rmoretti, it helps a lot!

[Anonymous]

set_dof is to set the movable degrees of freedom. If you want to fix a particular dof, you leave it unspecified. (https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/d1/dd2/symmetry.html#Symmetry_definitions) The value given is the initial value – movers and protocols can modify that value later in the process.

[Author]

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