project3d#

summary#

Create a stack of 2d projections at either random angles or from angles and shifts (optionally CTF applied) provided in a star file.

Optionally adds Gaussian noise to a specified SNR.

cli options#

interactive options#

input_reconstruction

The 3D reconstruction from which projections are calculated.

project_based_on_star

  • Angles from input .star file? If yes, angles and shifts will be obtained from an input star file, if not they will be made on a grid.

ouput_projection_stack

  • The output image stack, containing the 2D projections.

pixel_size

  • Pixel size of input images in Angstroms.

mask_radius

  • Radius of a circular mask to be applied to the final reconstruction in Angstroms.

wanted_SNR

  • Wanted SNR. The ratio of signal to noise variance after adding Gaussian noise and before masking.

padding

  • Padding factor. Factor determining how much the input volume is padded to improve projections.

my_symmetry

  • The assumed symmetry of the particle to be reconstructed.

apply_mask

  • Should the particles be masked with the circular mask?

add_noise

  • Should the Gaussian noise be added?

max_threads

  • Max. threads to use for calculation.