PyMOL tutorial 3 : Publication Quality Images

Описание

Expand the description for timings. - https://github.com/PyMOL-Ross
This is an introduction to making atomic selections and using commands in PyMOL
This is a rough edit from a tutorial.
Links
https://pymolwiki.org/index.php/Publication_Quality_Images
https://pymolwiki.org/index.php/Png
https://pymolwiki.org/index.php/Gallery

from the start : a little intro, running scripts and 'get_view'
00:04:37 : saving images, antialiasing, draw and ray
00:09:16 : image resolutions and dpi (dots per inch)
00:12:50 : reducing your ray time with 'hash_max'
00:16:10 : defaults and options and modes
00:21:13 : Interested in sticks
00:23:05 : Interested in cartoons
00:24:57 : Interested in topology
00:25:55 : Interested in surfaces
00:29:47 : Show hydrophobic
00:32:19 : Make Slices
00:35:18 : Binding Pocket representation
00:38:17 : QuteMol like images
00:39:46 : David Goodsell like images

00:04:37
####### key command
get_view

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

#######
ray # add shadows, white alpha-channel
# ray will use your current window dimensions, however . . .
# ray x, y (pixels)
ray 2400, 2400

00:09:16 #have a look at
https://pymolwiki.org/index.php/Publication_Quality_Images
#or
https://pymolwiki.org/index.php/Png

#######
00:12:50 # Blimey! my ray command takes a long time!!
get hash_max
set hash_max, 200 # test best for your machine

#######
00:16:10 # Image options
reinitialize
fetch 1nqu, async=0
util.cbc
as cartoon
set hash_max, 400
select none

# What are the defaults
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
get ray_trace_mode
set ray_trace_mode, 0
set ray_trace_mode, 1
set ray_trace_mode, 2
set ray_trace_mode, 3

# alter line thikness
get ray_trace_gain
set ray_trace_gain, 1

#######
00:21:13 # Interested in sticks
reinitialize
fetch 1nqu, async=0
util.cbc
as sticks
get stick_radius
set stick_radius = 1
set valence, 0
# or
set stick_radius = 1.5
set stick_radius = 2

#######
00:23:05 # Interested in cartoons
reinitialize
fetch 1nqu, async=0
util.cbc
as cartoon
cartoon loop
cartoon rect
cartoon oval
cartoon tube
cartoon automatic

# change secondary structure allocation
select c. C & i. 85-109
alter c. C & i. 85-109, ss='L'
as cartoon

# other options
set cartoon_fancy_helices=1
set cartoon_flat_sheets = 0
set cartoon_smooth_loops = 1

#######
00:24:57 # 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

#######
00:25:55 # 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 )
set hash_max, 400
ray

get spec_power
set spec_power = 200
get spec_refl
set spec_refl=1.5
get surface_quality
set surface_quality, 2
ray

See other examples at
https://pymolwiki.org/index.php/Gallery
00:29:47 : Show hydrophobic
00:32:19 : Make Slices
00:35:18 : Binding Pocket representation
00:38:17 : QuteMol like images
00:39:46 : David Goodsell like images