embed¶
parameters controlling protein embedding
Single-valued attributes:
no_orient: if true, do not alter orientation of protein; z-axis of protein coordinate system is assumed to be membrane normal (default: False)
q_tolerance: tolerance for net charge neutralization (default: 0.0001)
xydist: distance from perimeter of protein to box edge in x and y (Å) (default: 15)
zdist: distance from perimeter of protein to box edge in z (Å) (default: 20)
margin: distance from any protein atom in which no lipid atoms are permitted when embedding (Å) (default: 2.4)
z_head_group: VMD atomselect string defining head-group of z-axis
z_tail_group: VMD atomselect string defining tail-group of z-axis
z_ref_group: VMD atomselect string defining a center of mass at a specific z