Evaluate_FSCs

Evaluate FSCs

Purpose

This program allows you to evaluate reconstructions against its phantom. The comparison is performed through the Fourier Shell Correlation as implemented by Bsoft. The program can be used as a wrapper to bresolve (Bsoft) for computing a single FSC or several FSCs can be computed for an ensemble of similar reconstructions. In this case, statistical measures are returned about the FSCs.

Usage

$ evaluate_FSCs ...

Parameters

• `` The phantom must be a Xmipp voxel volume, the reconstruction can be either a single Xmipp voxel volume or a selection file with several voxel volumes. In case a selfile is given it must contain all reconstructions which are to be evaluated
• `` Name of the output file. The content of this file depends on the command use
• -sampling_rate [Tm1] = Sampling rate of the volumes (supposed to be the same) in Angstroms/pixel
• `` Use this option to compute the average resolution (frequency at which the FSC first falls below 0.5) of a set of volumes. If this option is used no output file is generated and therefore it is not necessary to provide the option-o
• `` Similar to the previous option but the whole FSC is returned. The average FSC as well as the maximum and minimum values in the set for each frequency are stored in the output file
• `` This option computes for every pair of volumes (one coming from the set 1 (-r) and another coming from the set 2 (this option)): FSC1 as the FSC of the volume in the first set, FSC2 as the FSC of the volume in the second set. Finally, it computes FSC2-FSC1. The output is the average difference at each frequency as well as its standard deviation

Examples and notes

Compute the FSC between two volumes

$ evaluate_FSCs -p volume1.vol -r volume2.vol -sampling_rate 3.5 -o FSC.txt

To plot this result you may use

$ gnuplot
$ gnuplot> set xrange [0:0.07]
$ gnuplot> set xlabel "Frequency (1/Angstroms)"
$ gnuplot> set ylabel "FSC"
$ gnuplot> plot "FSC.txt" u 1:2 w l

Compute the average resolution of an ensemble of volumes

$ evaluate_FSCs -p phantom.vol -r selfile_with_volumes.sel -sampling_rate 3.5 -compute_average_resolution

Compute the average, minimum and maximum FSC of an ensemble of volumes

$ evaluate_FSCs -p phantom.vol -r selfile_with_volumes.sel -sampling_rate 3.5 -compute_average_FSC -o FSC.txt 

To plot this result you may use

$ gnuplot
$ gnuplot> set xrange [0:0.07]
$ gnuplot> set xlabel "Frequency (1/Angstroms)"
$ gnuplot> set ylabel "FSC"
$ gnuplot> plot "FSC.txt" u 1:2 title "Average" w l, "FSC.txt" u 1:3 title "Minimum" w l, 
"FSC.txt" u 1:4 title "Maximum" w l

Compare the FSCs of two ensembles of volumes

$ evaluate_FSCs -p phantom.vol -r selfile_with_volumes1.sel -sampling_rate 3.5 \
-compare_two_sets selfile_with_volumes2.sel -o FSC.txt

To plot this result you may use

$ gnuplot
$ gnuplot> set xrange [0:0.07]
$ gnuplot> set xlabel "Frequency (1/Angstroms)"
$ gnuplot> set ylabel "FSC difference"
$ gnuplot> plot "FSC.txt" u 1:2 title "Average" w l,
"FSC.txt" u 1:3 title "Average-Std.Deviation" w l,
"FSC.txt" u 1:4 title "Average+Std.Deviation" w l

--Main.AlfredoSolano - 29 Jan 2007