Basic parameters
-fiber_diffraction:layer_lines inputs/fiber.dat #File containing fiber diffraction layer lines
-fiber_diffraction:a 27 #number of units
-fiber_diffraction:b 5 #number of turns
-fiber_diffraction:p 2.9 #If specified, subunit rise is taken from input, otherwise is calculated by the program
-fiber_diffraction:resolution_cutoff_low 0.0833333333 #Resolution cutoff 12Å
-fiber_diffraction:resolution_cutoff_high 0.3333333333 #Resolution cutoff 3Å
-fiber_diffraction:rfactor_refinement If set R factor instead of chi2 is used in scoring and derivatives calculations
#Additional parameters [in most cases there is no need to change them]
-fiber_diffraction::b_factor 20.0 #Atomic B-factor
-fiber_diffraction::b_factor_solv 400 #temperature factor that accounts for the disordered solvent
-fiber_diffraction::b_factor_solv_K 0.4 #scale factor that adjust average solvent scattering intensity

-fiber_diffraction:qfht_K1 2.0 #Hankel transform K1 parameter
-fiber_diffraction:qfht_K2 2.2 #Hankel transform K1 parameter
-edensity:sc_scaling 0.92 #Hankel transform K1 parameter

-fiber_diffraction:grid_r 256 #Grid size r, should be bigger than radius of molecule
-fiber_diffraction:grid_z 128 #Grid size z, should be bigger than molecule span in z direction
-fiber_diffraction:grid_phi 128 #Grid size phi, change if higher accuracy is needed
-fiber_diffraction:output_fiber_spectra Saves simulated intensities to a file

./make_helix_denovo.py -p 2.9 -n 40 -v 5 -u 27

• -p - helical rise
• -u - number of units
• -v - number of turns
• -n - number of subunits in a fibril
• -o - name of a symmetry definition file [OPTIONAL]
• -r - name of a virtual residues file [OPTIONAL]

Output:

• helix_denovo.sdef - contains symmetry information
• virtuals.pdb - contains virtual residues coordinates

Free and work set from fiber diffraction layer lines are generated using the following application

./bin/FiberDiffractionFreeSet.linuxgccrelease @flags

where flags file contains following arguments:
-fiber_diffraction:layer_lines inputs/fiber.dat #File containing fiber diffraction layer lines
-fiber_diffraction:a 27 #number of units
-fiber_diffraction:b 5 #number of turns
-fiber_diffraction:p 2.9 #If specified, subunit rise is taken from input, otherwise is calculated by the program
-fiber_diffraction:resolution_cutoff_low 0.0833333333 #Resolution cutoff 12Å
-fiber_diffraction:resolution_cutoff_high 0.3333333333 #Resolution cutoff 3Å
-fiber_diffraction:radius 33.3 #Fibrillar Radius in Å

Running command:

./inputs/minirosetta.linuxgccrelease @flags_fad

Four inputs files are required (apart from target sequence and fragment files). Example files for running simulations of bacteriophage viruses are as follows:

• Flags file
• Topology broker
• All-atom scoring patch that contains weight information
• Electron density-based scoring

The following command line executes symmetrical docking guided by electron density-based scoring function.
make_helix_denovo.py can be used to generate symmetry definition files.
Running command:

./inputs/Symdock.linuxgccrelease @flags_docking

Two inputs files are required to run simulations:

• Flags file
• Electron density-based scoring

Symmetrical comparative modeling on fibrillar template is run through the RosettaCM protocol of Rosetta.
Running command:

./inputs/rosetta_scripts.linuxgccrelease @flags_cm

Three inputs files are necessary to run simulations. The following example was used to run simulations of hibiscus latent Singapore virus:

• Flags file
• XML script that contains structure files and symmetry definition