Differences between revisions 6 and 7
Revision 6 as of 2012-11-19 23:03:54
Size: 2090
Editor: JiaFang
Comment:
Revision 7 as of 2012-11-19 23:05:25
Size: 3947
Editor: JiaFang
Comment:
Deletions are marked like this. Additions are marked like this.
Line 22: Line 22:

Below is an example script carrying out the steps described above:

{{{
#!/bin/bash

set echo on

# Predict parameters
# predict_helical_params("bdb:rerun//exports/home/pawel/elmar_small2_repeat/rerun/big_stack7", 27.6, 166.5, 1.84, outfile='predictedparams_bigstack7.txt')

COUNTER0=0
COUNTER1=1

MAXIT=1

mkdir RTR2
mkdir RTR2/shift0

sxheader.py bdb:/exports/home/pawel/elmar_small2_repeat/rerun/big_stack7 --params=active --one
cp consavg3.hdf RTR2/shift0/volfshift.hdf
sxheader.py bdb:/exports/home/pawel/elmar_small2_repeat/rerun/big_stack7 --params=xform.projection --import='predictedparams_bigstack7.txt'

while [ $COUNTER0 -lt 10 ]; do
        mpirun -np 56 -hostfile nodelist -wdir `pwd` sxihrsr.py bdb:/exports/home/pawel/elmar_small2_repeat/rerun/big_stack7 RTR2/shift$COUNTER0/volfshift.hdf RTR2/rotation$COUNTER1 cyl70mask.hdf --vol_ali --function="[.,helical_userfuncs,helical_act_elmar_mask]" --dp=27.6 --dphi=166.5 --apix=1.84 --rmin=0 --rmax=128.8 --fract=0.66 --maxit=$MAXIT --MPI --CTF --sym=c1 || exit
        sxheader.py bdb:/exports/home/pawel/elmar_small2_repeat/rerun/big_stack7 --params=xform.projection --export=RTR2/rotation$COUNTER1/params_disks$COUNTER1.txt

        mpirun -np 56 -hostfile nodelist -wdir `pwd` sxihrsr.py bdb:/exports/home/pawel/elmar_small2_repeat/rerun/big_stack7 RTR2/rotation$COUNTER1/fvheli.hdf RTR2/shift$COUNTER1 cyl70mask.hdf --maxit=1 --dp=27.6 --dphi=166.5 --apix=1.84 --rmin=0 --rmax=128.8 --fract=0.66 --searchxshift=36.8 --MPI --function="[.,helical_userfuncs,helical_act_elmar_mask]" --npad=2 --CTF --sym=c1 || exit
        sxheader.py bdb:/exports/home/pawel/elmar_small2_repeat/rerun/big_stack7 --params=xform.projection --export=RTR2/shift$COUNTER1/params_shifts$COUNTER1.txt

        let COUNTER1=COUNTER1+1
        let COUNTER0=COUNTER0+1
done
}}}

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. Each iteration consists of an alignment step followed by x-shift determination step., and the output of the alignment step serves as the starting structure for the x-shift determination step, and the output of the x-shift determination step serves as the starting structure of the alignment step of the next iteration. BRBR

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

      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=c1BRBR

      Determination of x-shift is activated by --searchxshift flag in sxihrsr: BRBR

      mpirun -np 56 -hostfile nodelist -wdir pwd sxihrsr.py bdb:some_stack starting_model.hdf output_directory mask.hdf --maxit=1 --dp=27.6 --dphi=166.5 --apix=1.84 --rmin=0 --rmax=128.8 --fract=0.66 --searchxshift=36.8 --MPI --function=[.,helical_userfuncs,helical_act_elmar_mask] --npad=2 --CTF --sym=c1

Below is an example script carrying out the steps described above:

set echo on

# Predict parameters
# predict_helical_params("bdb:rerun//exports/home/pawel/elmar_small2_repeat/rerun/big_stack7", 27.6, 166.5, 1.84, outfile='predictedparams_bigstack7.txt')

COUNTER0=0
COUNTER1=1

MAXIT=1

mkdir  RTR2
mkdir  RTR2/shift0

sxheader.py bdb:/exports/home/pawel/elmar_small2_repeat/rerun/big_stack7 --params=active --one
cp consavg3.hdf RTR2/shift0/volfshift.hdf
sxheader.py bdb:/exports/home/pawel/elmar_small2_repeat/rerun/big_stack7 --params=xform.projection --import='predictedparams_bigstack7.txt'

while [  $COUNTER0 -lt 10 ]; do
        mpirun -np 56 -hostfile nodelist -wdir `pwd` sxihrsr.py bdb:/exports/home/pawel/elmar_small2_repeat/rerun/big_stack7 RTR2/shift$COUNTER0/volfshift.hdf  RTR2/rotation$COUNTER1 cyl70mask.hdf --vol_ali --function="[.,helical_userfuncs,helical_act_elmar_mask]" --dp=27.6 --dphi=166.5 --apix=1.84 --rmin=0 --rmax=128.8 --fract=0.66 --maxit=$MAXIT --MPI --CTF --sym=c1 || exit
        sxheader.py bdb:/exports/home/pawel/elmar_small2_repeat/rerun/big_stack7 --params=xform.projection --export=RTR2/rotation$COUNTER1/params_disks$COUNTER1.txt

        mpirun -np 56 -hostfile nodelist -wdir `pwd` sxihrsr.py bdb:/exports/home/pawel/elmar_small2_repeat/rerun/big_stack7 RTR2/rotation$COUNTER1/fvheli.hdf RTR2/shift$COUNTER1 cyl70mask.hdf --maxit=1 --dp=27.6 --dphi=166.5 --apix=1.84  --rmin=0 --rmax=128.8  --fract=0.66 --searchxshift=36.8 --MPI --function="[.,helical_userfuncs,helical_act_elmar_mask]" --npad=2 --CTF --sym=c1 || exit
        sxheader.py bdb:/exports/home/pawel/elmar_small2_repeat/rerun/big_stack7 --params=xform.projection --export=RTR2/shift$COUNTER1/params_shifts$COUNTER1.txt

        let COUNTER1=COUNTER1+1
        let COUNTER0=COUNTER0+1
done

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