Documentation for the Denovo Symmetry Definiton file creation script.

Author:

Ingemar André

Metadata

Last edited Aug 20 2010 by Ingemar André. Code by Ingemar Andre.

Code and Demo

All the code is contained in the Python script src/apps/pilot_apps/andre/make_symmdef_file_denovo.py.

Purpose

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.

Options

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

Expected Outputs

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.