lunduniversity.lu.se

Denna sida på svenska This page in English

Running examples

Running examples

Overview Installation Running examples Benchmark Andre group

Example commands

Fiber diffraction flags

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

Generating symmetry definition files

./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

Generating free set

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

Fold-And-Dock simulations

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:

Low-resolution symmetrical docking

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:

Comparative modeling on fibrillar template

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: