Name

sxproject3d - generate a set of quasi-uniformly distributed projections of a volume

Usage

Usage in command lines:

sxproject3d.py volume stack <maskfile> --delta=angular_step --method=S --phiEqpsi=Minus --symmetry=c1 --angles=angles.txt --CTF=ctf.txt --noise=s

Usage in python programming:

project3d(volume, stack, mask = None, delta = 5, method = "S", phiEqpsi = "Minus", symmetry = "c1", listagls = None , listctfs = None, noise = None)

• Note: angles are in SPIDER convention.

Input

volume.hdf

input volume, can be either cubic or rectangular. In the case of rectangular volume, xy-size should be equal or less than the z-size.

mask.hdf

optional mask volume to be applied to the input volume before projections are calculated

delta

angular spacing of Eulerian angles

method

method of generating quasi-uniformly distributing Eulerian angles: 'P' Penczek '94 algorithm, theta angle is changing in steps of delta (default) or 'S' Saff helical method

phiEqpsi

if set to 'Minus' (default), then each of the Eulerian angles psi will be set to -phi. This results in neighboring projections having similar in-plane orientations. Otherwise, psi is set to zero.

angles

optional text files with projection directions (phi, theta, psi, sx, sy) (in SPIDER convention).

noise

add Gaussian noise with standard deviation s and zero mean CTF::optional text file with ctf parameters to be used ot modify the projections

symmetry

point group symmetry, projections are generated only to cover the asymmetric unit, see even_angles

Output

stack.hdf

stack with projections of the volume, attributes phi, theta, psi are set to appropriate angles (in SPIDER convention), and translations sx and sy are set to zero.

Note

project3d can be also used as a function in python code, in which case volume and mask can be in-core objects, stack has to be set to None, and the command will return an in-core stack of projections.

Reference

• Penczek, P., Grassucci, R. A. and Frank, J.: The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo electron microscopy of biological particles. Ultramicroscopy 53:251-270, 1994.
• Saff, E. B., Kuijlaars, A. B. J., 1997. Distributing many points on a sphere. Mathematical Intelligencer 19:5-11, 1997.
• Baldwin, P.R., Penczek, P.A.: The transform class in SPARX and EMAN2. J. Struct. Biol., 2007.
• Penczek, P.A., Renka, R. and Schomberg, H.: Gridding-based direct Fourier inversion of the three-dimensional ray transform. J. Opt. Soc. Am. A. 21:499-509, 2004.

Method

Gridding interpolation is used

Author / Maintainer

Pawel A. Penczek

Keywords

category 1

APPLICATIONS

category 2

FOURIER

Files

applications.py,sxproject3d.py

Bugs

None. It is perfect.