Correct_bfactor

correct_bfactor

Purpose

This utility may be used to sharpen a map. 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 (JMB, 2003);
2. Based on the fall-off in a reference map (possible obtained using xmipp_convert_pdb2vol);
3. application of a user-provided (ad hoc) B-factor.

Usage

$ correct_bfactor ...

Use one of the following three options

• `` Use automated B-factor fit acc. to (Rosenthal & Henderson, 2003)
• `` Fit a B-factor using a reference map (possibly obtained using convert_pdb22vol)
• `` Use a user-provided B-factor (usually negative!)

Parameters

• `` Volume to sharpen
• `` Output volume
• `` Pixel size (in Angstroms)
• `` Maximum resolution to apply B-factor (in Angstrom)
• -fit_minres [d15>] = Low-resolution limit for fit in -auto or -ref options (in Angstrom)
• -fit_maxres [dmaxres>] = High-resolution limit for fit in -auto or -ref options (in Angstrom)

Examples and notes

Sharpen a map using the automated procedure:

$ correct_bfactor -i input_volume.vol -o output_volume.vol -auto -sampling 2.8 -maxres 10

Besides the output volume, a text file calledoutput_volume.vol.guinier is created with the corresponding Guinier plots of the input volume, snr-weighted volume, corrected volume and reference volume/Wilson plateau. This file may be visualized using for examplegnuplot.

Bibliography

P.B. Rosenthal and R. Henderson, Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy, J. Mol. Biol. 333 (2003), pp. 721–745