Name

sxhelical_demo - Carry out various SPARX commands for helical demo script.

Usage

Helicise the atom coordinates of input pdb file 3MFP_1SU.pdb according to input helical symmetry parameters and write resulting file to rnew.pdb:

sxhelical_demo.py 3MFP_1SU.pdb rnew.pdb --heli --dp=27.6 --dphi=166.5

Generate three micrographs from reference volume tmp.hdf, where each micrograph contains one projection of a long filament with distortion from CTF and pixel size 1.84. The resulting micrographs are written to output directory mic:

sxhelical_demo.py tmp.hdf mic --generate_micrograph --CTF --apix=1.84

Generate noisy cylinder ini.hdf with radius 35 pixels and box size 100 by 100 by 200:

sxhelical_demo.py ini.hdf --generate_noisycyl --boxsize="100,100,200" --rad=35

Generate rectangular 2D mask mask2d.hdf with width 60 pixels and image size 200 by 200 pixels:

sxhelical_demo.py mask2d.hdf --generate_mask --masksize="200,200" --maskwidth=60

Apply the x-shift of the 2D alignment parameters stored in the headers of the images in bdb:adata, normalize using average and standard deviation outside the mask, and output the new images to bdb:data. The applied x-shift is always integral, and none integral x-shifts will simply be truncated to an integer before it is applied to the image:

sxhelical_demo.py bdb:adata bdb:data mask2d.hdf --applyparams

Options

Helicise atom coordinates

--heli

Helicise the atom coordinates of input pdb file according to input helical symmetry parameters.

--dp

Helical symmetry parameter rise in Angstroms (applicable only to --heli option).

--dphi

Helical symmetry parameter azimuthal rotation in degrees (applicable only to --heli option).

Generate micrograph

--generate_micrograph

Generate three micrographs where each micrograph contains one projection of a long filament.

--CTF

Apply CTF induced distortion to generated micrographs. Default is False. (applicable only to --generate_micrograph option).

--apix

pixel size in Angstroms. Default is -1. (applicable only to --generate_micrograph option).

--rand_seed

Integer. The seed used for generating random numbers (default 14567) for adding noise to the generated micrographs. (applicable only to --generate_micrograph option).

--Cs

Microscope Cs (spherical aberation). Default is 2.0. (applicable only to --generate_micrograph option).

--voltage

Microscope voltage in KV. Default is 200.0. (applicable only to --generate_micrograph option).

--ac

Amplitude contrast (percentage, default=10). (applicable only to --generate_micrograph option).

Generate noisy cylinder

--generate_noisycyl

Generate initial volume of noisy cylinder.

--boxsize

String containing x , y, z dimensions (separated by comma) in pixels (applicable only to --generate_noisycyl option). Default is "100,100,200"

--rad

Radius of initial volume in pixels. Default is 35.

Generate 2D rectangular mask

--generate_mask

Generate 2D rectangular mask.

--masksize

String containing x and y dimensions (separated by comma) in pixels of the mask to generate (applicable only to --generate_mask option). Default is "200,200"

--maskwith

Width of rectangular mask in pixels (default is 60). (applicable only to --generate_mask option).

Apply x-shift alignment parameters

--applyparams

Apply the centering parameters to input stack, normalize using average and standard deviation outside the mask, and output the new images to output stack.

Author / Maintainer

Jia Fang

Keywords

category 1

APPLICATIONS

Files

sparx/bin/sxhelical_demo.py

Maturity

beta

works for author, often works for others.