Name

sxhelicon_utils.py - Various utility functions for helical reconstruction

Usage

"Helicise pdb file and save the result to a new pdb file"

sxhelicon_utils.py 3MFP_1SU.pdb rnew.pdb --helicisepdb --nrepeats=50 --dp=27.6 --dphi=166.715

"Helices input volume and save the result to output volume"

sxhelicon_utils.py input_vol.hdf output_vol.hdf --helicise --dp=27.6 --dphi=166.5 --fract=0.65 --rmax=70 --rmin=1 --apix=1.84 --sym='c1'

"Generate two lists of image indices used to split segment stack into halves for helical fsc calculation."

sxhelicon_utils.py bdb:big_stack --hfsc='flst_' --filament_attr=filament

"Map of filament distribution in the stack"

sxhelicon_utils.py bdb:big_stack --filinfo=info.txt

The output file will contain four columns:

• 1 2 3 4

first image number last image number number of images in the filament name

"Generate disks from filament based reconstructions"

sxheader.py stk.hdf --params=xform.projection --import=params.txt

mpirun -np 2 sxhelicon_utils.py stk.hdf --gendisk='bdb:disk' --ref_nx=100 --ref_ny=100 --ref_nz=200 --apix=1.84 --dp=27.6 --dphi=166.715 --fract=0.67 --rmin=0 --rmax=64 --function="[.,nofunc,helical3c]" --sym="c1" --MPI

"Stack disks based on helical symmetry parameters"

sxhelicon_utils.py disk_to_stack.hdf --stackdisk=stacked_disks.hdf --dphi=166.5 --dp=27.6 --ref_nx=160 --ref_ny=160 --ref_nz=225 --apix=1.84

"Do helical symmetry search"

mpirun -np 3 sxhelicon_utils.py volf0010.hdf outsymsearch --symsearch --dp=27.6 --dphi=166.715 --apix=1.84 --fract=0.65 --rmin=0 --rmax=92.0 --datasym=datasym.txt --dp_step=0.92 --ndp=3 --dphi_step=1.0 --ndphi=10 --MPI

Input

"Generate two lists of image indices based on filament membership used to split segment stack into halves for helical fsc calculation."

hfsc

File prefix followed by '_even' and '_odd' under which the two lists of image indices will be stored.

filament_attr

Attribute in the image header under which filament identification is stored.

"Helicise pdb file and save the result to a new pdb file"

helicisepdb

Helicise pdb file and save the result to a new pdb file

nrepeats

Number of time the helical symmetry will be applied to the input file. The default is 50.

"Helicise input volume and save the result to output volume"

input_volume

Name of input volume

output volume

Name under which helicised volume will be saved

helicise

Helicise input volume and save results to output volume. Point-group symmetry is applied both before and after helicising.

"Map of filament distribution in the stack"

filinfo

Store in an output text file infomration about distribution of filaments in the stack.

"Generate disks from filament based reconstructions"

gendisk

Name of file under which generated disks will be saved to

CTF

CTF correction

maxerror

proportional to the maximum amount of error to tolerate between (dp/new_pixel_size) and int(dp/new_pixel_size ), where new_pixel_size is the pixel size calculated when the option --match_pixel_rise flag is True.

new_pixel_size

desired pixel size of the output disks. The default is -1, in which case there is no resampling (unless --match_pixel_rise flag is True).

match_pixel_rise

calculate new pixel size such that the rise is approximately integer number of pixels given the new pixel size. This will be the pixel size of the output disks.

"Stack disks based on helical symmetry parameters"

stackdisk

Name of file under which output volume will be saved to.

"Do helical symmetry search"

datasym

Text file to which new helical symmetry parameters are written

ndp

In symmetrization search, number of delta z steps equas to 2*ndp+1

dp_step

delta z (Angstroms) step for symmetrization

ndphi

In symmetrization search,number of dphi steps equas to 2*ndphi+1

dphi_step

dphi step for symmetrization

"Options common to multiple functionalities"

dp

delta z - translation in Angstroms

dphi

delta phi - rotation in degrees

apix

pixel size in Angstroms

rmin

minimal radius for hsearch (Angstroms)

rmax

maximal radius for hsearch (Angstroms)

fract

fraction of the volume used for helical search

sym

point-group symmetry of the structure

function

name of the reference preparation function

ref_nx

nx=ny volume size (for options stackdisk and gendisk)

ref_ny

ny of output volume size. Default is ref_nx

ref_nz

nz volume size - computed disks will be nx x ny x rise/apix

Keywords

category 1

APPLICATIONS

Files

sparx/bin/sxhelicon_utils.py

Maturity

beta

works for author, often works for others.