Aph2img

crystal_aph2img

Purpose

This program converts APH files into real space images. It performs a DISCRETE but NOT FAST Fourier transform. The input APH file is obtained by executing the MRC programorigmerg.com ( the fileorigmerg.aph contains the 2D Crystal spots of the projections that result from a complete tilt series). The output file is an image that can be handled using xmipp_programs as xmipp_show.

Usage

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Parameters

• ``

Parameter file

• `` APH file from origmerg (origmerg.aph)
• `` single proyection in real space
• `` maxIQ
• Output cells no1 1 = number of unit cell (1 by default) (x_direc,y_direc)
• `` Magnitude of vector a
• `` Magnitude of vector b
• `` Angle between vector a and b
• `` Angle taxa (calculated using emtilt)
• `` Angle tilt (calculated using emtilt)
• `` Sampling rate (A/pixel)
• `` must be given in degrees (x_shift, y_shift)
• `` mrc_label
• `` if contrast must be inverted set this to zero
• `` volume size in real space (x_dim,y_dim)
• `` Scale Factor
• `` Generate symmetrical reflection
• `` Symmetry Group (P4, P4212, P1)

An example of the command line, along with examples of the input and output files are shown below:

Command line

crystal_aph2img -i

Notes

In the parameter file the following fields are normally adjust: APH file, a_mag, b_mag, a_b_ang, taxa, tilt, sampling rate, Phase Shift, mrc_label, Cell Size and Symmetry group. The following fields are normally set to constant values: Output cells no (1 1), Keep Contrast (1), Generate symmetrical reflection (1).

--Main.JavierRodriguez - 24 Sep 2007