Conversion scripts for FREALIGN
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gather_imagic.com
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A shell script that converts IMAGIC alignment parameters to FREALIGN parameters. It is assumed that class averages were calculated and angles/shifts were assigned to these averages. The script will have to be adapted to work with the latest IMAGIC version as the output text from IMAGIC commands will have changed. The main value of this script is the conversion of angles/shifts to FREALIGN's conventions.


convertm.com
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A shell script to run convertm.exe. convertm.exe converts a Spider parameter file into FREALIGN parameters. The Fortran code convertm.f will have to be compiled:

gfortran -o convertm.exe convertm.f

Included is an example parameter file, spider_params.spi, which contains a list of all the relevant parameters needed by FREALIGN.


gather_spi.com, gather_spi_boot.com, frealignprep.com
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Shell scripts to convert Spider parameters generated by the random conical tilt reconstruction. The script frealignprep.com has to be executed first to generate input files for the later scripts. The _boot script should be run when shifts are not known and only the angles are available for each particle (from the random conical tilt procedure). A rough reconstruction using these angles can then be used to determine shifts.
