fitctf

• This program estimates CTF parameters in batch. The results should be checked in CTFIT

Usage

• fitctf <input file> [sf=<SF File>] [apix=<a/pix>] [V=<voltage>] [Cs=<spher aber>] [over=<oversampling>] [acmax=<max AC>] [acfix=<max AC>] [Bhint=<B factor] [Bfix=<B factor>] [Bexp] [debug]

Parameters

• <input file>	File containing boxed particles to be evaluated
  [sf=<SF File>]	File containing estimated 1D structure factor for this specimen
  [apix=<a/pix>]	Angstroms/pixel in the image
  [V=<voltage>]	Voltage in KV
  [Cs=<spher aber>]	Spherical aberation in mm
  [over=<oversampling>]	eg - 2 -> 2x oversampling
  [acmax=<max AC>]	eg - .1 is max 10% ac, default is .14
  [acfix=<max AC>]	fixed amplitude contrast
  [Bhint=<B factor]	A strong hint for the B-factor, strictly optional
  [Bfix=<B factor>]	Force the B factor to a specific value
  [Bexp]	Use an exponential 'B-factor' rather than a Gaussian
  [debug]	Verbose debugging output

  Typical usage: fitctf jj1023.hed groel.sm

Description

This program will attempt to determine the CTF parameters of a a set of particles. It will write the result into a .tnf file, which can then be read into ctfit. The results of this program should always be manually verified in ctfit. This program is just designed to save the user a little manual effort.

If you have a fairly small model (size in pixels < 128) or are very far from focus, you might consider using the oversampling option with a value of 2 or 3.

Please note that this program uses an exceptionally inefficient algorithm. However, there is a lot of embedded 'magic' in this routine. It is designed to be functional, not fast.

EMAN Manual page, generated Mon Jan 8 17:35:59 2007