yasspa [molecule] [template] [cutoff distance]
An option to define the secondary structure of a protein, given a set of CA coordinates. The template molecule must reside in the users database. It is normally supplied in the $ODAT directory as an O type file. Current templates are alpha.o and beta.o corresponding to alpha-helices and beta-strands. These coordinates are the central members of a cluster analysis (Jones, unpublished) using a 0.5Å cutoff (the default value to YASSPA). To define alpha-helices use this 0.5Å cutoff. For beta-strands use 0.8Å (this is because beta-strands show more deviation from the central cluster). If it does not exist, The option creates a residue property [mol]_residue_2ry_struc. The following example colours a molecule depending on secondary structure:
mol a yasspa a alpha 0.5 yasspa a beta 0.8 pain_prop res_2ry = ' ' yellow pain_prop res_2ry = alpha red pain_prop res_2ry = beta green ca ; end