# When preparing images, write a script (copy and paste commands) to a 
# text file, to allow you to recreate the image again in the future!!

reinitialize 
fetch 2chb, async=0
run niceify2.pml

dist hbsc, organic, sc, mode=2
dist hbbb, organic, bb, mode=2
color cyan, hbsc
color magenta, hbbb
hide labels

# key command
get_view

set_view (\
    -0.253887773,    0.819441199,    0.513858318,\
     0.903327703,    0.390773684,   -0.176850557,\
    -0.345724672,    0.419285655,   -0.839441359,\
     0.000526633,   -0.000106305,  -72.495323181,\
    27.612598419,   45.513324738,   19.832817078,\
    54.909694672,   90.036903381,  -20.000000000 )

draw			# quick anti-aliasing
get antialias
set antialias, 2
set antialias, 1

set_view (\
     0.804116547,   -0.290881038,    0.518437326,\
    -0.557278991,   -0.672452390,    0.487060457,\
     0.206952378,   -0.680573046,   -0.702836454,\
     0.000325076,    0.000658320, -103.680000305,\
    -4.907163143,   35.938167572,   15.877665520,\
    72.554985046,  134.784973145,  -20.000000000 )
ray			# add shadows, white alpha-channel

# ray will use your current window dimensions, however . . .
ray x, y 	(pixels)
ray 2400, 2400
ray 1200, 2400
ray 2400, 1200

#####################################

https://pymolwiki.org/index.php/Publication_Quality_Images

How do I create a X DPI image using PyMol's 'ray' command?
ray 2400, 2400

rayVal = inches * DPI
therefore

ray 576,576   # 8inch * 72dpi
save ray576.png
ray 800,800   # 8inch * 100dpi; or a 4inch * 200 DPI image; or 1x800.
save ray800.png
ray 2400,2400 # 8inch * 300dpi; 6"x400dpi, etc...
save ray2400.png

Then use graphics software to scale to an appropriate dimension
I recommend the free software for image manipulation
Gimp
Inkscape
Fiji (is just imageJ)

ALTERNATIVELY
https://pymolwiki.org/index.php/Png # however this is a little redundent

ray first!
png dpi150, dpi=150
png dpi300, dpi=300
png dpi600, dpi=600

# combine both methods
png dpi300-ex, width=2400, height=2400, dpi=300, ray=1

#####################################

Blimey! my ray command takes a long time!!

rein 
fetch 1nqu, type=pdb1 
split_states 1nqu
bg_color white
orient
util.cbc
remove ! polymer

ray
	Ray: render time: 45.55 sec. = 79.0 frames/hour (258.18 sec. accum.).

# use more memory for image processing? (make sure you don’t crash it!)
get hash_max
	get: hash_max = 100

set hash_max, 200
ray 
	Ray: render time: 15.56 sec. = 231.4 frames/hour (273.74 sec. accum.).

set hash_max, 400
ray 
	Ray: render time: 12.10 sec. = 297.6 frames/hour (285.84 sec. accum.).

set hash_max, 800
ray 
	Ray: render time: 15.51 sec. = 232.2 frames/hour (301.34 sec. accum.).



#####################################
# Image options
#####################################
reinitialize
fetch 1nqu, async=0
run ../0-Setup/niceify2.pml
set hash_max, 400
select none

What are the defaults
ray

get spec_reflect
get ray_shadows
get ray_trace_color
get ray_trace_fog
get depth_cue
get ray [tab]

ray

set spec_reflect, off
set ray_shadows, off
set ray_trace_color, black
set ray_trace_fog, 0
set ray_opaque_background, on

ray

#####################################
# Ray tracing modes
#####################################
reinitialize
fetch 1nqu, async=0
run ../0-Setup/niceify2.pml
set hash_max, 400
select none

get ray_trace_mode

set ray_trace_mode, 0
ray 


set ray_trace_mode, 1	# line thickness independent of magnification
ray 			# this is nice when zoomed in, but thick lines at low mag
ray 2400, 2400		# line thickness is dependent on resolution

# want to tweek line thickness?
get ray_trace_gain
set ray_trace_gain, 1		# show example, dont mess too much!
set ray_trace_gain, 0.12

set ray_trace_mode, 2
ray
ray 2400, 2400

set ray_trace_mode, 3
ray
ray 2400, 2400

###########################
# Interested in sticks
###########################
reinitialize
fetch 1nqu, async=0
run ../0-Setup/niceify2.pml
set hash_max, 400
select none


get valence
as sticks

set valence, 0
set valence, 1


get stick_radius
set stick_radius = 1

set valence, 0
util.cbc
set stick_radius = 1.5
set stick_radius = 2

also available
get sphere_scale

###########################
# Interested in cartoons
###########################
reinitialize
fetch 1nqu, async=0
run ../0-Setup/niceify2.pml
set hash_max, 400
select none

as cartoon
cartoon loop
cartoon rect
cartoon oval
cartoon tube
cartoon automatic

# dependent on pymols internal validation of secondary structure
# not always correct

select c. C & i. 85-109
alter c. C & i. 85-109, ss='L'
as cartoon

set cartoon_fancy_helices=1
set cartoon_flat_sheets = 0
set cartoon_smooth_loops = 1

###########################
# Interested in topology
###########################
as cartoon
color red, ss h
color marine, ss s
color yellow, ss l+''
set cartoon_smooth_loops = 1
set cartoon_flat_sheets = 0


###########################
# Interested in surfaces
###########################

reinitialize
fetch 1nqu, async=0
remove solvent + inorganic
orient 
bg_color white
color red, ss h
color marine, ss s
color yellow, ss l+''
as surface
set_view (\
     0.545457602,   -0.442487806,    0.711814880,\
    -0.747303188,    0.127776876,    0.652082741,\
    -0.379491985,   -0.887624860,   -0.260975480,\
    -0.000065712,   -0.000067554, -100.300979614,\
   140.149993896,   11.831371307,  127.861839294,\
    52.274650574,  148.330902100,  -20.000000000 )

#####   get_view
set hash_max, 400
ray
save 4-Images-RayTracing-surf-norm.png

get spec_power
set spec_power = 200
ray
save 4-Images-RayTracing-surf-sp200.png

get spec_refl
set spec_refl=1.5
ray
save 4-Images-RayTracing-surf-sr1.5.png

get surface_quality
set surface_quality, 2
ray
save 4-Images-RayTracing-surf-sq2.png

# additionally
set solvent_radius, 2.0
set surface_solvent = on

###########################################################################################
https://pymolwiki.org/index.php/Gallery
#############################################
#  Show hydrophobic
#############################################

reinitialize
fetch 1nqu
orient 
bg_color white
set hash_max, 400
as cartoon,all
color gray,all
remove solvent

select hydrophobes, (r. ala+gly+val+ile+leu+phe+met)
show spheres, (hydrophobes and (!name c+n+o))
color orange,hydrophobes
disable hydrophobes
show surface, polymer
set transparency, 0.5
show sticks, organic
color black, organic


set_view (\
     0.663258672,    0.559077382,    0.497514009,\
    -0.666870713,    0.743225574,    0.053842291,\
    -0.339663506,   -0.367489606,    0.865782797,\
     0.000000000,    0.000000000, -114.893775940,\
   161.621994019,   17.474000931,  137.559997559,\
    66.865669250,  162.921905518,  -20.000000000 )

ray
png shhy-ray

get spec_power
get spec_refl
get surface_quality


set spec_power = 1
set spec_refl= 1
set surface_quality, 0
ray
png shhy-ray110

# 118 sec   # DONT DO THIS ONE!!
set spec_power = 200
set spec_refl=1.5
set surface_quality, 2
set antialias, 2
ray 2400
png shhy-ray112

#############################################
#  Make Slices
#############################################

reinitialize
fetch 1nqu, async=0
orient 
bg_color white
remove solvent
set hash_max, 400

# must disable depth cue and shadows
set depth_cue, 0
set ray_shadows, 0
set ray_trace_mode, 0

# this controls the z depth of the slice plane
# (sets it halfway between the clipping planes)
fraction = 0.42
view = cmd.get_view()
near_dist = fraction*(view[16]-view[15])
far_dist = (view[16]-view[15]) - near_dist
cmd.clip("near", -near_dist)

# render opaque background image
as surface
set ray_interior_color, grey80
set opaque_background
set surface_color, white
ray
save Images-MakeSlices-image_back.png

cmd.clip("near", near_dist)
cmd.clip("far", far_dist)

 # render the foreground image
as cartoon
util.cbc
unset opaque_background
ray
save Images-MakeSlices-image_front.png

# open Images-MakeSlices*


#############################################
#  Binding Pocket representation
#############################################

reinitialize
fetch 1nqu, tmp, async=0
bg_color white
remove solvent
set hash_max, 400

extract prot, polymer
extract lig, organic
select bb, bb.
select sc, sc. + n. ca + PRO/N 
as cartoon, bb
show sticks, sc
util.cbc
color black, lig
show sticks, lig
util.cnc

select lig1, lig & c. A

set surface_carve_cutoff, 4.5
set surface_carve_selection, lig1
set surface_carve_normal_cutoff, -0.1

show surface, prot within 8 of lig1
set two_sided_lighting
set transparency, 0.5
orient lig1
zoom lig1, 2

set surface_color, white
set surface_type, 2
distance hbond, lig1, prot, mode=2
color grey50, hbond
set ray_shadows, 0
ray
png pocket1

#####  a little further out?

zoom lig1, 10
select pocket2, br. lig1 expand 5
select pocket, pocket2 & ! name c+o+n + /*//*/PRO`*/N
delete pocket2
hide sticks, sc
hide lines, sc
show sticks, pocket
turn z, -45
turn x, -90
ray
png pocket2

#############################################
#  QuteMol like images
#############################################

reinitialize
fetch 1nqu, async=0
bg_color white
remove solvent
set hash_max, 400

set_color oxygen, [1.0,0.4,0.4]
set_color nitrogen, [0.5,0.5,1.0]
as spheres
util.cbaw
bg white
set light_count,8
set spec_count,1
set shininess, 10
set specular, 0.25
set ambient,0
set direct,0
set reflect,1.5
set ray_shadow_decay_factor, 0.1
set ray_shadow_decay_range, 2
unset depth_cue
# for added coolness
# set field_of_view, 60
ray

#############################################
#  David Goodsell like images
#############################################

reinitialize
fetch 1nqu, tmp, async=0
bg_color white
set hash_max, 400

as sticks
set valence, 0
set stick_radius = 1.7

color lightblue, not org
color magenta, org
remove solvent

# set the view

set_view (\
     0.855354905,    0.057524908,    0.514838457,\
    -0.050117217,    0.998342931,   -0.028284293,\
    -0.515611708,   -0.001608965,    0.856820703,\
     0.000006188,   -0.000014648, -238.717636108,\
   153.867889404,    1.374834061,  136.634002686,\
   208.820083618,  268.618896484,  -20.000000000 )

# set the lights, ray tracing setttings
# to get the Goodsell-like rendering

unset specular
set ray_trace_gain, 0
set ray_trace_mode, 3
bg_color white
set ray_trace_color, black
unset depth_cue
ray