Lilien Lab
Department of Computer Science
Centre for Cellular and Biomolecular Research
University of Toronto

In order to find out what options you need to provide to the program, just execute it without providing any arguments. The following message should appear:

Data file not specified.
Usage:LBFGSCryoBayes.exe -i [mrc file] -o [analysis name]
  -i:       Specify the name of the input mrc file.
  -o:       Specify the name of the output analyses (no .mrc extension).
  -r:       Specify the rotation file to use.
  -p:       Specify the PSF file to use.
  -s:       Specify the mrc file with the starting model (Optional).
  -eps:     Specify epsilon improvement in log likelihood for continued iterations 
	    (Optional. Default=.1).
  -nGeo:    Specify number of subdivisions for Geodesic points. Default=3).
  -psisDeg: Specifies the granularity (in degrees) of the rotations around 
	    the z-axis. Default=6).
  -nIter:   Number of iterations for each annealing run. (Optional. Default = 10)
  -reg:     Regularizer penalty value. (Optional. Default = 1e-6. Suggested 
            1e-3 when no psf correction used)
  -free:    Do not fix image 1 to some position. (Optional. Default = fix 1 image)
  -pLamda:  Prior lambda for spatial prior (Default = 0.1)
  -fixRot:  Fix rotations to those provided in rotations file (Only applies 
            when rotation file is provided as argument.)
  -sProj:   Save Projections.
  -minSD:   Minimum standard deviation during annealiing (Default = 0.1).
  -sSD:     Starting standard deviation during annealiing (Default = 20.0).

You can download data from our Download page to try this software. In each of the datasets provided, there is a perl file, run.pl, which can be used to call the program. Modify run.pl to specify the path of the executable and the path of the dataset, and execute run.pl.