Xmipp

xmipp_ctf_enhance_psd (v3.0)

Usage

Enhances the visibility of the Thon rings in a Power Spectrum Density (PSD).

See also
ctf_estimate_from_micrograph

Parameters

-i, --input <input_file>
Metadata with PSDs or a single PSD
--mode <mode=overwrite>
Metadata writing mode.
where <mode> can be:
  • overwrite Replace the content of the file with the Metadata
  • append Write the Metadata as a new block, removing the old one
-o, --output <output_file=>
Output file: metadata, stack, volume or image.
--oroot <root=>
Rootname of output individual images. Output image format can be set adding extension after rootname as ":ext".
--method <mth=filter>
Choose enhancing method
where <mth> can be:
  • filter <freq_low=0.05> <freq_high=0.2> <freq_decay=0.02> Ad hoc filters. The algorithm is fully described at this article The frequency limits define a raised-cosine bandpass filter, frequencies are normalized to 0.5
  • spht <N0=1> <NF=10> Spiral phase transform normalization. N0 and NF define the minimum and maximum number of fringes in the CTF

Output parameters

--dont_center
By default, the output is centered
--dont_log
Don't take log10 before working

Output mask parameters

--m1 <freq_low=0.025>
Low freq. for frequency mask, max 0.5
--m2 <freq_high=0.3>
High freq. for frequency mask, max 0.5

Examples and notes

xmipp_ctf_enhance_psd -i myPSD.psd -o myPSD_enhanced.psd

User's comments

%COMMENT{type="tableappend"}%

  • Raw PSD:
    this_psd.jpg

  • Enhanced PSD:
    this_psd_enhanced.jpg