################################################################################
# PyMOL script to make animation of displayed PDB file rotating 360 degrees
# about x-, y-, and z-axes. Mostly the biomolecule is in ribbons format, but
# also displayed in CPK spheres for a few arcs of the rotation. Output .png
# files are written out, and then glued into an animated gif by ImageMagik's
# "convert" program...or converted to .gif's then a .mpg via "makempeg"...
#
# Cameron Mura
# 06/02/2003
################################################################################

########### ENTER THE PATH TO YOUR "pymol_movies.py" HERE ###################
run /u1/cmura/FOR_OTHERS/PYMOL/pymol_movies.py

# reset the view and, optionally, set background color to white:
reset
#bg_color white

# load in sample PDB file:
load sample.pdb, sample

# make various selections:
# (in this case, the four chains of the tetramer and the backbone)
select chain_a = (sample and c;a)
select chain_b = (sample and c;b)
select chain_c = (sample and c;c)
select chain_d = (sample and c;d)
select backbone = (n;c,ca,o,n)
deselect

# first hide everything that's displayed...
hide everything

# use this next line to estimate structure for cartoon-making purposes 
# if you don't already have secondary structure declared in PDB file
# (i.e. missing HELIX and SHEET lines)
#util.ss (sample)

# make cartoon representation after setting some parameters for the 
# appearance of helices and loops:
set cartoon_fancy_helices=1
set cartoon_smooth_loops=1
cartoon auto, sample
show cartoon, sample

# color different chains:
color red, (chain_a)
color blue, (chain_b)
color salmon, (chain_c)
color slate, (chain_d)

# Here's a nice view that was selected because it's parallel to one 
# of the tetramer's 2-folds...
# Get your own custom view by orienting the display as you like and 
# then type "get_view". Then replace the set_view matrix below with the 
# output of that command...

### cut below here and paste into script ###
set_view (\
    -0.965603113,   -0.258433580,    0.028463041,\
     0.028288594,    0.004388066,    0.999581277,\
    -0.258451939,    0.966020942,    0.003072893,\
     0.000000000,    0.000000000, -242.078796387,\
    33.639591217,   19.016521454,   52.659023285,\
   190.856765747,  308.240570068,    0.000000000 )
### cut above here and paste into script ###