/usr/share/pymol/scripts/metaphorics/fedora.pml is in pymol-data 1.8.4.0+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 | # quash output
feedback disable, all, everything
# assign secondary structure (if not already assigned)
dss preserve=1
# define selections (may need to be improved)
select protein, not hetatm
select ligand, not ( protein or hoh+wat/ )
select water, ( hoh+wat/ within 5 of ligand )
select contacts, byres ( protein within 4 of ligand )
# hide selection indicators
deselect
# customize settings
set sphere_scale, 0.25
set stick_radius, 0.1
set dot_width, 1.5
# display desired representations
hide
show spheres, ligand
show sticks, ligand or contacts
show cartoon, protein
show nonbonded, water
# draw hydrogen bonds
dist hbond, not ligand, ligand, mode=2
hide labels, hbond
# color protein by secondary structure
color white, protein and ss ''+L
color orange, protein and ss S
color magenta, protein and ss H
# disable color blending on cartoon
set cartoon_discrete_colors,1
# don't smooth loops -- let's see the real coordinates
set cartoon_smooth_loops, 0
set cartoon_flat_sheets, 0
# color visible atoms by type
util.cbag ligand
util.cbac contacts and not name ca
# now bind some zoom actions to F1-F4
cmd.set_key('F1',lambda :cmd.zoom())
cmd.set_key('F2',lambda :cmd.zoom("ligand",8))
cmd.set_key('F3',lambda :cmd.zoom("ligand"))
cmd.set_key('F4',lambda :cmd.zoom("ligand",-8))
# orient system along principal axes
orient
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