Xmipp

xmipp_volume_correct_bfactor (v3.0)

Usage

Sharpen a volume by applying a negative B-factor The high-resolution features are enhanced, thereby correcting the envelope functions of the microscope, detector etc. Three modes are available:

  1. An automated mode based on methodology developed by Rosenthal and Henderson

  1. Based on the fall-off in a reference map (possibly obtained using xmipp_volume_from_pdb)

  1. An user-provided (ad hoc) B-factor

See also
volume_enhance_contrast volume_from_pdb resolution_fsc

Parameters

-i, --input <input_file>
Input file: metadata, stack, volume or image.
--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
--label <image_label=image>
Label to be used to read/write images.
--auto
Use automated B-factor fit in flat Wilson region Note: do not use the automated mode for maps with resolutions lower than 12-15 Angstroms!
or --ref <fn_ref> <mode=bfactorref>
Fit B-factor according to the reference
where <mode> can be:
  • bfactorref Fit B-factor
  • allpoints Adjust power spectrum to reference
or --adhoc <B>
Use a user-provided (negative) B-factor

Specific parameters

--sampling <float>
Pixel size of the input volume (in Angstroms/pixel)
--maxres <float>
High-resolution limit for B-factor correction (in Ang.)
-o <filename>
Output file Name with corrected volume
--fit_minres <f=15>
Low-resolution limit (in Ang.) for fit in --auto or --ref
--fit_maxres <f=-1>
High-resolution limit (in Ang.) for fit in --auto or --ref, -1 means maximum resolution
--fsc <fscFile=>
FSC file produced by xmipp_resolution_fsc

Examples and notes

xmipp_correct_bfactor -i volume.vol -o correctedVolume.vol --auto --sampling 1.4 --maxres 10
To plot the Guinier file you may use:
gnuplot
set xlabel "d^(-2)"
plot "correctedVolume.vol.guinier" using 1:2 title "log F" with line, "correctedVolume.vol.guinier" using 1:4 title "Corrected log F"with line

User's comments

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