# general environment
bg_color white
#space cmyk
set fetch_path, /tmp
log_open /tmp/pymol_log.pml
set retain_order

load ~/.pymol/chimera_colors.pml

# interface
set overlay, 1

# performance
set async_builds, on
set max_threads, 8
set cache_mode
set defer_builds_mode, 3
set hash_max, 500

# raytrace
set depth_cue, 0
set ray_opaque_background, false
set orthoscopic, 0
#set ray_shadow, false 
set spec_reflect, 0.25
set antialias, 1
set surface_quality, 1
set ray_trace_mode, 0

# hide nonbonded and nbsphreres
set nonbonded_transparency, 1
set nb_spheres_size, 0

# stick settings
set valence, 0

# cartoon
set cartoon_gap_cutoff, 1
set cartoon_side_chain_helper, 1
set cartoon_discrete_colors, on
#set cartoon_highlight_color, gray
set cartoon_oval_length, 0.8


# spheres
set sphere_scale, 0.5

# custom colors
set_color sodium, [1.0, 0.87, 0.37]
set_color potassium, [0.0, 0.5, 1.0]

# bigger dashes
set dash_gap, .35
set dash_length, .3

# shortcuts
set_key F1, toggle sticks, solvent
set_key F2, toggle sticks, (r. POPC or r. POP) and not hydrogen
set_key F3, toggle spheres, inorganic and (n. NA or n. K)
set_key F4, toggle spheres, n. CL

set_key F9, set depth_cue
set_key F10, set depth_cue, off
set_key F11, ray 800,800
set_key F12, ray 1600,1600



alias clean, hide everything, hydrogen or n. 1M* or n. 2M* or n. MC*
alias sf_as_sticks_HCN4, show sticks, residue 478-484 and (not hydrogen or (hydrogen and neighbor (elem O+N+S))) and not (n. 1M* or n. 2M* or n. MC*); hide cartoon, resi 479-483;
alias sf_as_sticks_HCN4_sele, show sticks, sele and residue 478-484 and (not hydrogen or (hydrogen and neighbor (elem O+N+S))) and not (n. 1M* or n. 2M* or n. MC*); hide cartoon, resi 479-483;
alias sideview_HCN4, hide sticks; hide everything, polymer and chain B+D; select polymer and chain A+C; sf_as_sticks_HCN4_sele; deselect;

alias sf_as_sticks_HCN1, show sticks, residue 357-362 and (not hydrogen or (hydrogen and neighbor (elem O+N+S))) and not (n. 1M* or n. 2M* or n. MC*); hide cartoon, resi 358-361
alias ionwatch, hide everything; show cartoon; show spheres, n. NA or n. K; sf_as_sticks_HCN4; hide everything, ID 1-1899; hide everything, ID 3799-5695 
alias dockfix, as sticks, bonded and not polymer