pymol snippts for pretty pictures of large set of molecules

boomerang effect movie

files=("$@")

reverse() {
    # first argument is the array to reverse
    # second is the output array
    declare -n arr="$1" rev="$2"
    for i in "${arr[@]}"
    do
        rev=("$i" "${rev[@]}")
    done
}

reverse files rfiles

batch=50

convert -delay 3 -loop 0 ${files[@]} animated.test.gif
convert -delay 5 -loop 0 ${rfiles[0]} animated.wait.gif
convert -delay 3 -loop 0 ${rfiles[@]} animated.test2.gif

convert animated.test.gif animated.wait.gif animated.test2.gif test.gif

pymol animation

mset 1 x360
util.mroll(1,360,2)
set ray_trace_frames=1
set cache_frames=0
mclear
mpng mov

pymol view effects

viewport 1024, 768

set ray_trace_gain, 0.1;
set ray_shadow_decay_factor, 0.1;
set ray_shadow_decay_range, 2;

set antialias, 2;
set reflect,0.5;

set light_count,20;
set spec_count,1;
set shininess, 100;
set specular, 1;
set direct,0;
set reflect,1.5;

pymol view without molecule border

# https://combichem.blogspot.com/2013/12/beautiful-rendereing-of-small-molecules.html

load my_molecule.xyz

bg_color white
color grey50, elem c
preset.ball_and_stick(selection='all', mode=1)
set ray_trace_mode, 0

ray