for amino acid scores and Weight
for predicted secondary structure scores
These two weights determine the relative contribution of amino acid similarity and predicted secondary structure similarity to the profile-profile hidden Markov model used in PROMALS. These weights can be set to any positive values. Larger weight means larger contribution of this score to the total alignment score. The default and recommended values are 0.8 for amino acid scores and 0.2 for secondary structure scores. These values were optimized on SCOP domain pairs with less than 20% sequence identity.