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77 lines
2.2 KiB
Plaintext
77 lines
2.2 KiB
Plaintext
# general environment
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bg_color white
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#space cmyk
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set fetch_path, /tmp
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log_open /tmp/pymol_log.pml
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set retain_order
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load ~/.pymol/chimera_colors.pml
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# interface
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set overlay, 1
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# performance
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set async_builds, on
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set max_threads, 8
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set cache_mode
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set defer_builds_mode, 3
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set hash_max, 500
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# raytrace
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set depth_cue, 0
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set ray_opaque_background, false
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set orthoscopic, 0
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#set ray_shadow, false
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set spec_reflect, 0.25
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set antialias, 1
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set surface_quality, 1
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set ray_trace_mode, 0
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# hide nonbonded and nbsphreres
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set nonbonded_transparency, 1
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set nb_spheres_size, 0
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# stick settings
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set valence, 0
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# cartoon
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set cartoon_gap_cutoff, 1
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set cartoon_side_chain_helper, 1
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set cartoon_discrete_colors, on
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#set cartoon_highlight_color, gray
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set cartoon_oval_length, 0.8
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# spheres
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set sphere_scale, 0.5
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# custom colors
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set_color sodium, [1.0, 0.87, 0.37]
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set_color potassium, [0.0, 0.5, 1.0]
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# bigger dashes
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set dash_gap, .35
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set dash_length, .3
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# shortcuts
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set_key F1, toggle sticks, solvent
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set_key F2, toggle sticks, (r. POPC or r. POP) and not hydrogen
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set_key F3, toggle spheres, inorganic and (n. NA or n. K)
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set_key F4, toggle spheres, n. CL
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set_key F9, set depth_cue
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set_key F10, set depth_cue, off
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set_key F11, ray 800,800
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set_key F12, ray 1600,1600
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alias clean, hide everything, hydrogen or n. 1M* or n. 2M* or n. MC*
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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;
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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;
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alias sideview_HCN4, hide sticks; hide everything, polymer and chain B+D; select polymer and chain A+C; sf_as_sticks_HCN4_sele; deselect;
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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
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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
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alias dockfix, as sticks, bonded and not polymer
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