File:4gms colors.png

Prepared in response to a pymol-users thread from 11/30/2018-12/5/2018 about the appearance of transparency in a published figure.

Script to reproduce:

bg_color white
fetch 4gms, async=0

# hemagglutinin selections
select ha, chain A
select l130, ha and resi 133-138
select l150, ha and resi 155-163
select h190, ha and resi 187-196
select l220, ha and resi 225-228
select loops, l130 or l150 or h190 or l220

# antibody selection
select h2, chain H and resi 51-59
deselect

# basic view
hide everything
as cartoon, ha
as cartoon, h2
cartoon tube

# colors
color orange, h2
color palecyan, ha
color deepteal, loops

set_view (\
    -0.718157351,    0.514449000,   -0.468602538,\
    -0.667115033,   -0.317360103,    0.673974276,\
     0.198008969,    0.796632588,    0.571111977,\
     0.000045628,   -0.000060942,  -75.169761658,\
    20.388980865,  -23.567779541,   38.543788910,\
    52.026283264,   98.326217651,  -20.000000000 )

set ray_opaque_background, 1
png 4gms_colors.png, height=800, width=800, ray=1