Symmetry definition in standalone

Case number:845829-2008173
Topic:Crash/Hang
Opened by:lelivre
Status:Open
Type:Question
Opened on:Sunday, September 29, 2019 - 09:49
Last modified:Monday, September 30, 2019 - 18:51

When uploading on of symmetry examples from Rosetta demos, I encountered this error:

args passed:
'./FolditStandalone'
'-symmetry:symmetry_definition'
'2akf_symmdef.dat'
'-symmetry:initialize_rigid_body_dofs'
'-in:file:s=2akf_INPUT.pdb'
args used:
'./FolditStandalone'
'-interactive_game'
'standalone'
'-boinc_url'
'NO_SERVER'
'-dont_update'
'-dont_quickstart'
'-symmetry:symmetry_definition'
'2akf_symmdef.dat'
'-symmetry:initialize_rigid_body_dofs'
'-in:file:s=2akf_INPUT.pdb'
'-resources'
'cmp-resources-e4328842f71e24d69469859ca008eea9/resources'
'-database'
'cmp-database-854915b461ab56af5e112d277aefce4d/database'
'-interactive:interactive_residue_types'
'-ignore_unrecognized_res'
'-out:level'
'200'
Initializing translator using: cmp-resources-e4328842f71e24d69469859ca008eea9/resources/locale/foldit.zs.po
starting the init thread!..
SoundTheme::load: cmp-resources-e4328842f71e24d69469859ca008eea9/resources/sounds/organic_01
loading: cmp-resources-e4328842f71e24d69469859ca008eea9/resources/sounds/organic_01/rotamer_land_00.ogg
loading: cmp-resources-e4328842f71e24d69469859ca008eea9/resources/sounds/organic_01/rotamer_land_01.ogg
loading: cmp-resources-e4328842f71e24d69469859ca008eea9/resources/sounds/organic_01/rotamer_land_02.ogg
loading: cmp-resources-e4328842f71e24d69469859ca008eea9/resources/sounds/organic_01/rotamer_land_03.ogg
loading: cmp-resources-e4328842f71e24d69469859ca008eea9/resources/sounds/organic_01/rotamer_land_04.ogg
loading: cmp-resources-e4328842f71e24d69469859ca008eea9/resources/sounds/organic_01/rotamer_land_05.ogg
SVM classifier successfully loaded
Feature list successfully loaded
Valid classifier feature list
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting weight of master jump ( jump-id=5 ) to 1.0 (was undefined)
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting jump_group JUMPGROUP2: [master 5] 7:0 9:0
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting weight of master jump ( jump-id=1 ) to 1.0 (was undefined)
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting jump_group JUMPGROUP3: [master 1] 2:0 3:0
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting weight of master jump ( jump-id=5 ) to 1.0 (was undefined)
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting jump_group JUMPGROUP2: [master 5] 7:0 9:0
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting weight of master jump ( jump-id=1 ) to 1.0 (was undefined)
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting jump_group JUMPGROUP3: [master 1] 2:0 3:0
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting weight of master jump ( jump-id=5 ) to 1.0 (was undefined)
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting jump_group JUMPGROUP2: [master 5] 7:0 9:0
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting weight of master jump ( jump-id=1 ) to 1.0 (was undefined)
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting jump_group JUMPGROUP3: [master 1] 2:0 3:0
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting weight of master jump ( jump-id=5 ) to 1.0 (was undefined)
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting jump_group JUMPGROUP2: [master 5] 7:0 9:0
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting weight of master jump ( jump-id=1 ) to 1.0 (was undefined)
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting jump_group JUMPGROUP3: [master 1] 2:0 3:0
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting weight of master jump ( jump-id=5 ) to 1.0 (was undefined)
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting jump_group JUMPGROUP2: [master 5] 7:0 9:0
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting weight of master jump ( jump-id=1 ) to 1.0 (was undefined)
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting jump_group JUMPGROUP3: [master 1] 2:0 3:0
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting weight of master jump ( jump-id=5 ) to 1.0 (was undefined)
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting jump_group JUMPGROUP2: [master 5] 7:0 9:0
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting weight of master jump ( jump-id=1 ) to 1.0 (was undefined)
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting jump_group JUMPGROUP3: [master 1] 2:0 3:0
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting weight of master jump ( jump-id=5 ) to 1.0 (was undefined)
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting jump_group JUMPGROUP2: [master 5] 7:0 9:0
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting weight of master jump ( jump-id=1 ) to 1.0 (was undefined)
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting jump_group JUMPGROUP3: [master 1] 2:0 3:0
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting weight of master jump ( jump-id=5 ) to 1.0 (was undefined)
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting jump_group JUMPGROUP2: [master 5] 7:0 9:0
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting weight of master jump ( jump-id=1 ) to 1.0 (was undefined)
^[[0mcore.conformation.symmetry.SymmData: ^[[0mSetting jump_group JUMPGROUP3: [master 1] 2:0 3:0
^[[0m^[[1m^[[31m
ERROR: Anchor outside the subunit...
ERROR:: Exit from: /home/folditbuilder/foldit/rosetta-interactive/source/src/core/conformation/symmetry/util.cc line: 467
^[[0m^[[35m./FolditStandalone(print_backtrace()+0x26) [0x3caf496]
./FolditStandalone(utility::exit(std::string const&, int, std::string const&, int)+0x102) [0x45ecf12]
./FolditStandalone(core::conformation::symmetry::set_fold_tree_from_symm_data(core::kinematics::FoldTree const&, core::conformation::symmetry::SymmData&, std::map, std::allocator > >)+0xc25) [0x4353f55]
./FolditStandalone(interactive::util::symmetrize_fold_tree(core::kinematics::FoldTree&)+0x148) [0x21787d8]
./FolditStandalone(interactive::util::setup_star_jumps_and_cuts(core::pose::Pose&, ObjexxFCL::FArray1D const&, ObjexxFCL::FArray1D const&)+0x2f0) [0x2178be0]
./FolditStandalone(interactive::util::game_pose_from_pdb(core::pose::Pose&, std::istream&, boost::shared_ptr)+0x22d) [0x217a45d]
./FolditStandalone(interactive::util::game_pose_from_pdb(core::pose::Pose&, std::string const&, boost::shared_ptr)+0x17d) [0x217a83d]
./FolditStandalone(standalone::application::novice::BuildingBlockPanel::IdealLoop::IdealLoop(std::string const&)+0x41a) [0x1f3911a]
./FolditStandalone(standalone::application::novice::BuildingBlockPanel::init_building_block_gallery()+0x20b) [0x1f39b3b]
./FolditStandalone(standalone::application::novice::BuildingBlockPanel::BuildingBlockPanel(interactive::util::access_ptr, interactive::util::access_ptr, interactive::util::owning_ptr, interactive::util::access_ptr)+0x41d) [0x1f3a63d]
./FolditStandalone(standalone::application::novice::BlueprintPanel::BlueprintPanel(interactive::util::access_ptr, interactive::util::access_ptr, interactive::util::owning_ptr, interactive::util::owning_ptr)+0x1508) [0x1f301b8]
./FolditStandalone(standalone::application::novice::StandaloneApplication::init_gui_blueprint_panel()+0x71) [0x1d868b1]
./FolditStandalone(standalone::application::novice::StandaloneApplication::init_gui()+0x2b5) [0x1daec35]
./FolditStandalone(standalone::application::novice::StandaloneApplication::init()+0x101) [0x1dc66f1]
./FolditStandalone(interactive::util::Thread::thread_entry_func()+0x2d) [0x216020d]
./FolditStandalone(interactive::util::Thread::pthread_startup_helper(void*)+0x9) [0x2160479]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x76ba) [0x7fb4d02da6ba]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x6d) [0x7fb4cfb9341d]
^[[0m

Please, help me to figure out the case. Thanks for your attention.

(Sun, 09/29/2019 - 09:49  |  2 comments)


rmoretti's picture
User offline. Last seen 9 hours 39 min ago. Offline
Joined: 01/15/2010
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It's hard to say for certain, but I'm guessing that in the symmetry definition file you're loading, the anchor_residue line is specifying a residue number which is not in the asymmetric unit.

One thing to be cautious about is that the anchor_residue number (like most residue numbers in Rosetta/Foldit which don't have an associated chain letter), is in something called "pose numbering", not PDB numbering. (This is the first number you see in the Segment Information panel you get when you press Tab.) So the first residue in the structure is 1, the next is 2, going up without gaps and without restarting for new chains. -- I'm guessing you might have used PDB numbering with a structure that doesn't start the PDB numbering at 1.

bkoep's picture
User offline. Last seen 8 hours 4 min ago. Offline
Joined: 11/15/2012
Groups: None

Also, just want to clarify that anchor_residue must be N+1, where N is the number of residues in your asymmetric unit. This is unlike other Rosetta applications, which can tolerate an anchor_residue at other positions; in Foldit, anchor_residue must correspond to a "virtual residue" that is automatically appended at the C-terminus of your asymmetric unit.

For example, if you load a PDB with 100 residues, then the anchor_residue should be 101. Like rmoretti said, the pose numbering for your structure will be 1-100 (regardless of the numbering in your source PDB file); and then Foldit will append a virtual residue with number 101, which should be your anchor_residue.

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