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Short helpfile for action EMMI
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The input trajectory can be in any of the following formats: 

                  ATOMS - atoms for which we calculate the density map, typically all 
                          heavy atoms. For more information on how to specify lists of 
                          atoms see \ref Group 

The following arguments are compulsory: 

               GMM_FILE - file with the parameters of the GMM components 
              NL_CUTOFF - The cutoff in overlap for the neighbor list 
              NL_STRIDE - The frequency with which we are updating the neighbor list 
              SIGMA_MIN - minimum uncertainty 
             RESOLUTION - Cryo-EM map resolution 
              NOISETYPE - functional form of the noise (GAUSS, OUTLIERS, MARGINAL) 

In addition you may use the following options: 

  NUMERICAL_DERIVATIVES - ( default=off ) calculate the derivatives for these 
                          quantities numerically 
                  NOPBC - ( default=off ) ignore the periodic boundary conditions 
                          when calculating distances 
                NO_AVER - ( default=off ) don't do ensemble averaging in 
                          multi-replica mode 
                 SIGMA0 - initial value of the uncertainty 
                 DSIGMA - MC step for uncertainties 
              MC_STRIDE - Monte Carlo stride 
               ERR_FILE - file with experimental or GMM fit errors 
                OV_FILE - file with experimental overlaps 
           NORM_DENSITY - integral of the experimental density 
            STATUS_FILE - write a file with all the data useful for restart 
           WRITE_STRIDE - write the status to a file every N steps, this can be used 
                          for restart 
             REGRESSION - regression stride 
          REG_SCALE_MIN - regression minimum scale 
          REG_SCALE_MAX - regression maximum scale 
             REG_DSCALE - regression maximum scale MC move 
                  SCALE - scale factor 
                 ANNEAL - Length of annealing cycle 
            ANNEAL_FACT - Annealing temperature factor 
                   TEMP - temperature 
                  PRIOR - exponent of uncertainty prior 
        WRITE_OV_STRIDE - write model overlaps every N steps 
               WRITE_OV - write a file with model overlaps 


