Rosetta 3.3
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Last edited Aug 20 2010 by Ingemar André. Code by Ingemar Andre.
All the code is contained in the Python script src/apps/pilot_apps/andre/make_symmdef_file_denovo.py.
This script automatically creates symmetry definition files corresponding to the specified symmetry. It currently covers cyclical and dihedral symmetry.
Limitations This routine does not create symmetry definition files for all types of symmetries. These have to be made by hand, see the symmetry definition guide, or from a template by application of make_symmdef_file to a known protein complex.
Running the script without options give the possible range of options.
usage: make_symmdef_file_denovo.py [options] example: make_symmdef_file_denovo.py -symm_type cn -nsub 2 example: make_symmdef_file_denovo.py -symm_type dn -nsub 4 example: make_symmdef_file_denovo.py -symm_type dn -nsub 4 -slide_type RANDOM -slide_criteria_type CEN_DOCK_SCORE example: make_symmdef_file_denovo.py -symm_type cn -nsub 24 -subsystem common options: -symm_type (cn|dn) : The type of symmetry. Currently cyclic or dihedral symmetry -nsub <integer> : number of subunits -subsystem : Simulate a smallers subsystem. For cn 3 consecutive subunits are represented. For dn 6 subunits are represented 3 in the upper ring and 3 in the lower ring -slide_type (RANDOM|SEQUENTIAL|ORDERED_SEQUENTIAL) : Defines how a multidimensional slide should be performed. For dn symmetry there are two sliding directions. A slide can be done by randomly selecting a slide direction for each slide step (RANDOM), randomly deciding on which direction should be slided first but always sequentially go through both (SEQUENTIAL), or define the order yourself (ORDERED_SEQUENTIAL). RANDOM default -slide_criteria_type (CEN_DOCK_SCORE|FA_REP_SCORE|CONTACTS) : Defines what the criteria is for abandaning a slide. Either the CEN_DOCK_SCORE, FA_REP_SCORE or the number of contacts. CEN_DOCK_SCORE deafult -slide_criteria_val <string|float> : Sets the actual value when a slide move is abandoned given the criteria type. By default set to AUTOMATIC, which means that ROSETTA figures it out by itself. Really only useful for the CONTACTS type
A sample command line to generate a trimer. The same command was used to create the symmetry definition for the symmetric docking integration test (mini/test/integration/tests/symmetric_docking):
make_symmdef_file_denovo.py -symm_type cn -nsub 3
This gives rise to the following symmetry definition:
symmetry_name c3 subunits 3 recenter number_of_interfaces 1 E = 3*VRT0001 + 3*(VRT0001:VRT0002) anchor_residue COM virtual_transforms_start start -1,0,0 0,1,0 0,0,0 rot Rz 3 virtual_transforms_stop connect_virtual JUMP1 VRT0001 VRT0002 connect_virtual JUMP2 VRT0002 VRT0003 set_dof BASEJUMP x(50) angle_x(0:360) angle_y(0:360) angle_z(0:360)
The actual format of the symmetry definition file is described in the Symmetry User's Guide.