# set background color to white

bg_color white

# load pdb files:

load mth_p21.pdb, mth

## a good view down the 7-fold axis:
set_view (\
     0.557053328,    0.830005229,   -0.027990183,\
    -0.664286673,    0.425098091,   -0.614828587,\
    -0.498412430,    0.361086011,    0.788163424,\
     0.000000000,    0.000000000, -254.101638794,\
    41.177429199,   10.965770721,   63.651733398,\
   184.265167236,  338.903076172,    1.000000000 )

util.ss mth

hide everything, mth
set cartoon_fancy_helices=1
set cartoon_smooth_loops=0

cartoon auto, mth
show cartoon, mth

select hept1 = (mth and c;A,B,C,D,E,F,G)
select hept2 = (mth and c;H,I,J,K,L,M,N)
select mpd = (mth and resn MPD)
select ump = (mth and (resn U5P or resn URD))
select pho = (mth and name P)
show spheres, mpd
show spheres, ump
show spheres, pho

deselect

## Color various items...e.g., hept1 blue 
## hept2 red, carbon atoms in MPD yellow, etc.
color blue, hept1
color red, hept2
color yellow, (mpd and element c)
color grey, (ump and element c)

clip slab, 130

set antialias = 1
set gamma = 1.15
set orthoscopic = 1

# do ray-tracing and write out .png files
ray 800,600
png MthSmAP1_ribbons_and_ligands.png

## End PyMOL...
quit