= 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.

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