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Assign_multiple_CTFs

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Adrian Quintana edited this page Dec 11, 2017 · 1 revision

Assign multiple CTFs

Purpose

This program allows you to apply the Assign_CTF program succesively to a set of micrographs. Several microprocessors can be used at a time. The input micrograph can be in any format: Tiff, raw or downsampled raw. This program calls the apropriate sequence of programs (tiff2raw, downsample) until the corresponding downsampled image is reached. Furthermore, if the images are gzipped, the gunzip program is called.

The input files to this program must be in the same directory. For each input micrograph listed in the input selfile the following files must exist:

  • [image_filename].[ext] Input micrograph
  • [image_filename].sel Set of projection images extracted from this micrograph
  • [image_filename].pos Set of projection centers as produced byMark

The output files are written in the output directory (if none is provided the input one is used). All intermidiate files are written in the output directory and removed automatically at the very moment that they are not needed any more, in this way the minimum disk space is required.

For each micrograph the following files are created:

  • [image_filename].bat Batch for applying Assign_CTF to this micrograph
  • [image_filename]_assign_CTF.param Parameters for Assign_CTF for this micrograph
  • [image_filename]_ctf.param Parameters for Adjust_CTF for this micrograph
  • [image_filename]_arma[NNNNN].fft ARMA estimation for a certain piece of this micrograph
  • [image_filename]_ctf[NNNNN].fft Theoretical CTF estimation for that same piece

For each projection image[projection_name].[ext] it is created the filectf-[projection_name].[ext].fft which is the theoretical CTF estimation for the particle projection.

The correction of the CTF can be done either withCorrectPhase for correcting the phase or with IDR_ART for correcting the amplitude (this program needs that the phase is already corrected).

Usage


$ assign_multiple_CTFs -i [selfile] -tif -prm  [textfile] ...

Parameters

  • `` Input selfile with all the input micrographs
  • __OR__OR`` Kind of input images
  • `` Apply gunzip to the input micrograph before proceeding
  • `` Output directory
  • `` Parameters forAssign_CTF. The following parameters are not needed:
    • image
    • selfile
    • picked
    • ARMAfile
    • CTFfile
  • -proc [n1] = Number of processors to be used
  • `` Any of the Downsample parameters. The downsampling needed for the CTF correction may be different from the one you use. It is very important that there are no absolute zeros in the micrograph spectrum, i.e., if the antialiasing filter is too hard then there will be frequencies at which the micrograph spectrum is null and this fact is terrible for the ARMA estimation.
    • Some good downsampling parameters are``

Examples and notes

  • If you have marked several families in the micrograph, all selfiles and posfiles should be combined into a single sel and posfile

Example of application:


$ xmipp_assign_multiple_CTFs -i raw_images.sel -raw -unzip -odir ../CTF_Xmipp/Images/ \
-prm ../CTF_Xmipp/assign_CTF.prm -proc 2 -Xstep 3 -kernel sinc 95 15 &

where the content of the../CTF_Xmipp/assign_CTF.prm file is the following:


# Assign CTF parameters
N_horizontal=512
N_vertical=512
particle_horizontal=150
particle_vertical=150

# ARMA parameters
N_AR=24
M_AR=24
N_MA=20
M_MA=20

# Adjust CTF parameters
voltage=200
spherical_aberration=2
sampling_rate=3.27

--Main.AlfredoSolano - 16 Jan 2007

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