misc.py

def sign(x):
    if x > 0:
        return 1.0
    if x < 0:
        return -1.0
    return 0.0


def gp120_fusion():
    cen = com('chain A+C+E')
    axis = cen.normalized()
    cmd.load("/Users/sheffler/Downloads/gp120_trimer_model.pdb", "gp")
    alignc3('gp', tgtaxis=axis)
    cen2 = com('gp')
    l1 = cen.length()
    l2 = sign(cen.dot(cen2)) * cen2.length()
    rot('gp', axis, random.random() * 120.0)
    trans('gp', axis * (l1 - l2 + 100))
    cmd.remove("gp and not chain A")
    cmd.remove("not gp and not chain A+B")
    cmd.alter('gp', 'chain="C"')
    cmd.hide('ev')
    cmd.set('ribbon_radius', "7")
    cmd.set('ribbon_sampling', "3")
    cmd.show('rib')
    util.cbc()
    cmd.color("cyan", "chain A")
    cmd.color("green", "chain B")
    cmd.color("yellow", "chain C")
    makeicos("all", n=60)
    return axis


def gp120_fusion_oct():
    cen = com('chain B+J+L')
    axis = cen.normalized()
    cmd.load("/Users/sheffler/Downloads/gp120_trimer_model.pdb", "gp")
    alignc3('gp', tgtaxis=axis)
    cen2 = com('gp')
    l1 = cen.length()
    l2 = sign(cen.dot(cen2)) * cen2.length()
    rot('gp', axis, random.random() * 120.0)
    trans('gp', axis * (l1 - l2 + 85))
    cmd.remove("gp and not chain A")
    cmd.remove("not gp and not chain A+B")
    cmd.alter('gp', 'chain="C"')
    cmd.hide('ev')
    cmd.set('ribbon_radius', "7")
    cmd.set('ribbon_sampling', "3")
    cmd.show('rib')
    util.cbc()
    cmd.color("yellow", "chain C")
    makeoct("all", n=24)
    return axis