Create_micrograph

phantom_create_micrograph

Purpose

phantom_create_micrograph combines theProject andMicroscope to create a phantom micrograph. The program stores the micrograph with noise and CTF as well as the absolutely clean micrograph (with no CTF).

Usage

$ phantom_create_micrograph ...

[-ctf ] : a CTF description [-defocus_change <v=0%>] : change in the defocus value [-low_pass <w=0>] : low pass filter for noise before CTF [-noise <stddev=0>] : noise to be added [-after_ctf_noise] : generate noise after the CTF

Parameters

• `` Volume from which the micrograph will be created. Random projections of this volume will be created
• -o [rootname"micrograph"] = Each micrograph is stored in a separate directory under the names micrograph000, micrograph001. Inside each directory you will find the noisy and noiseless micrographs, alignment docfiles so that you can reconstruct with the generated particles, selfiles, and the set of scissored particles.
• -dim [dim2048] = Size of the micrograph, which is supposed to be square.
• -N [N1] = Number of micrographs to generate
• Any of the input parameters toMicroscope

Examples and notes

A typical use of this program is

$ phantom_create_micrograph -vol ../Src/Volumen-ccp4-35A_64.vol -density 20 \
      -ctf ../Src/ctf.ctfparam -noise 0.7 -after_ctf_noise

--Main.CoSS - 18 Dec 2008