# Pymol script to inspect Abl-Kinase
# Thomas R. Schneider
# 18/6/2013
delete all
load 1FPU.pdb
hide all
# All
create abl, chain A and resi 225-499
create lig, chain A and resi 1 
set_bond stick_radius, 0.1, all
color grey9, name C*
show sticks, lig
show spheres, lig
set sphere_scale, 0.25, (all)
show spheres, abl
show sticks, abl
scene F1, store
# STRETCH
hide all
create stretch, chain A and  resi 374-385
show sticks, stretch
scene F2, store
color green, stretch and (name ca or name c)
scene F3, store
# All 
hide all
show sticks, abl
color green, abl and (name ca or name c)
scene F4, store
hide sticks, abl and not (name n or name ca or name c)
color green,(name n)
scene F5, store, Backbone
# show ribbon, stretch
# set ribbon_color, green
# set ribbon_width, 7
# helix
hide all
create helix, chain A and resi 337-355
show sticks, helix and (name n or name ca or name c or name o)
color green, helix and (name c*)
color blue, name N
dist hbonds, helix and (name n or name o), helix and (name n or name o), mode=2
scene F6, store, alpha-helix
#
# beta sheet
hide all
create beta-sheet, chain A and (resi 301-305 or resi 311-316 or resi 267-273)
show sticks, beta and (name n or name ca or name c or name o)
color green, beta and (name c*)
color blue, name N
dist hbonds2,  beta and (name n or name o), beta and (name n or name o), mode=2
scene F7, store, beta-sheet
# 
hide all
show cartoon