Volume_correct_bfactor_v3

!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
2. Based on the fall-off in a reference map (possibly obtained using xmipp_volume_from_pdb)
3. An user-provided (ad hoc) B-factor

See also Volume_enhance_contrast_v3 Volume_from_pdb_v3 Resolution_fsc_v3

Parameters

$``: Input file: metadata, stack, volume or image. $--mode <modeoverwrite> where <mode> can be:

• • $--label <image_labelimage> $``: 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> <modebfactorref> where <mode> can be:
  • $ or``: Use a user-provided (negative) B-factor

Specific parameters $: Pixel size of the input volume (in Angstroms/pixel) $: High-resolution limit for B-factor correction (in Ang.) $``: Output file Name with corrected volume $--fit_minres <f15> $`--fit_maxres &lt;f`-1&gt; $`--fsc <fscFile`>

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

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