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1. Predict projection parameters based on geometrical consistency using helical symmetry parameters rise and azimuthal rotation.

    '''Command'''
   sxihrsr.py bdb:big_stack --predict_helical='predictedparams_bigstack7.txt' --dp=27.6 --dphi=166.5 --apix=1.84

2. Perform alignment of filament-based reconstructions and x-shift determination.
  . i. Make a directory where the output directories will go, and make a sub-directory shift0 in this directory.
  . ii. Copy the starting structure (may simply be a noisy cylinder) into shift0.
  . iii. Initialize projection parameters of the input stack to the predicted helical parameters.
  . iv. Run alignment of filament-based 3D reconstructions alternated with x-shift determination:<\br>

         Alignment of filament-based reconstructions is activated by the --vol_ali flag in sxihrsr:


         mpirun -np 56 -hostfile nodelist -wdir `pwd` sxihrsr.py bdb:some_stack starting_model.hdf output_directory mask.hdf --vol_ali --function=[.,helical_userfuncs,helical_act] --dp=27.6 --dphi=166.5 --apix=1.84 --rmin=0 --rmax=128.8 --fract=0.66 --maxit=1 --MPI --CTF --sym=c1

Geometrically Consistent IHRSR

The below describes the sequence of steps for carrying out helical refinement based on geometrical considerations arising from helical symmetry.

1. Predict projection parameters based on geometrical consistency using helical symmetry parameters rise and azimuthal rotation.

  • Command

  • sxihrsr.py bdb:big_stack --predict_helical='predictedparams_bigstack7.txt' --dp=27.6 --dphi=166.5 --apix=1.84

2. Perform alignment of filament-based reconstructions and x-shift determination.

  • i. Make a directory where the output directories will go, and make a sub-directory shift0 in this directory.
  • ii. Copy the starting structure (may simply be a noisy cylinder) into shift0.
  • iii. Initialize projection parameters of the input stack to the predicted helical parameters.
  • iv. Run alignment of filament-based 3D reconstructions alternated with x-shift determination:<\br>

    • Alignment of filament-based reconstructions is activated by the --vol_ali flag in sxihrsr:

      mpirun -np 56 -hostfile nodelist -wdir pwd sxihrsr.py bdb:some_stack starting_model.hdf output_directory mask.hdf --vol_ali --function=[.,helical_userfuncs,helical_act] --dp=27.6 --dphi=166.5 --apix=1.84 --rmin=0 --rmax=128.8 --fract=0.66 --maxit=1 --MPI --CTF --sym=c1

sxheliconlocal (last edited 2018-01-09 22:26:16 by penczek)