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pymolpy.snips
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pymolpy.snips
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snippet ao
abbr ao
alias ao
cmd.do("set_color oxygen, [1.0,0.4,0.4];")
cmd.do("set_color nitrogen, [0.5,0.5,1.0];")
cmd.do("remove solvent;")
cmd.do("as spheres;")
cmd.do("# the \"as\" command is a shortcut for show_as")
cmd.do("util.cbaw;")
cmd.do("# \"cba\" represents \"color by atom\". ")
cmd.do("# The last letter represents the colore of the carbon atom.")
cmd.do("bg white;")
cmd.do("# bg is an alias for bg_color or background color.")
cmd.do("set light_count,10;")
cmd.do("# light_count is the number of light sources. ")
cmd.do("# The max is 10. The defualt is 10.")
cmd.do("set spec_count,1;")
cmd.do("# Not documented on Wiki.")
cmd.do("set shininess, 10;")
cmd.do("# sets the shininess of the object.")
cmd.do("set specular,0.25;")
cmd.do("# Controls the amount of directly reflected light and not the shininess of the reflection.")
cmd.do("set ambient,0;")
cmd.do("# Controls the amount of ambient light. Default is 0. Ranges from -1 to 1.")
cmd.do("set direct,0; ")
cmd.do("# Not documented on Wiki.")
cmd.do("set reflect,1.5;")
cmd.do("# Controls the amount of light reflection and the effect that directional light has on shadows ")
cmd.do("# and the general lighting of the scene. Default value is 0.5.")
cmd.do("set ray_shadow_decay_factor, 0.1;")
cmd.do("set ray_shadow_decay_range, 2;")
cmd.do("set depth_cue, 0;")
cmd.do("ray;")
$0
snippet sas
abbr sas
alias sas
cmd.do("set surface_solvent, ${1:on}")
$0
snippet ellipcol
abbr ellipcol
alias ellipcol
cmd.do("set ellipsoid_color, ${1:red};")
$0
snippet sigdist
abbr sigdist
alias sigdist
cmd.do("set label_distance_digits, ${1:2};")
$0
snippet sigang
abbr sigang
alias sigang
cmd.do("set label_angle_digits, ${1:2};")
$0
snippet bs
abbr bs
alias bs
cmd.do("show sticks;")
cmd.do("set stick_radius, 0.12;")
cmd.do("set stick_ball, on;")
cmd.do("set stick_ball_ratio, 1.9;")
cmd.do("show nb_spheres;")
cmd.do("set nb_spheres_size=0.33;")
$0
snippet stack
abbr stack
alias stack
cmd.do("delete all;")
cmd.do("fetch ${1:4PCO}, type=pdb,async=0;")
cmd.do("select ${2:G2G3}, ( ((resi ${3:2} or resi ${4:3}) and chain A) or ((resi ${5:8} or resi ${6:9}) and chain B) );")
cmd.do("hide everything, element h; ")
cmd.do("remove not ${2:G2G3};")
cmd.do("bg_color white;")
cmd.do("show sticks;")
cmd.do("set stick_radius=0.14;")
cmd.do("set stick_ball, on; ")
cmd.do("set stick_ball_ratio,1.9;")
cmd.do("set_view (-0.75,0.09,0.66,-0.2,0.92,-0.35,-0.64,-0.39,-0.67,-0.0,-0.0,-43.7,7. 24,9.55,11.78,29.46,57.91,-20.0);")
cmd.do("hide everything, element H;")
cmd.do("select carbon1, element C and (resi ${4:3} or resi ${5:8}); ")
cmd.do("# select lower base pair;")
cmd.do("select carbon2, element C and (resi ${3:2} or resi ${6:9});")
cmd.do("#select upper base pair;")
cmd.do("color gray70,carbon1;")
cmd.do("color gray10,carbon2;")
cmd.do("space cmyk;")
cmd.do("distance hbond1,/${1:4PCO}//B/U`9/N3,/${1:4PCO}//A/G`2/O6;")
cmd.do("distance hbond2,/${1:4PCO}//B/U`9/O2,/${1:4PCO}//A/G`2/N1;")
cmd.do("distance hbond3,/${1:4PCO}//A/U`3/N3,/${1:4PCO}//B/G`8/O6;")
cmd.do("distance hbond4,/${1:4PCO}//A/U`3/O2,/${1:4PCO}//B/G`8/N1;")
cmd.do("color black, hbond1;")
cmd.do("color black, hbond2;")
cmd.do("color gray70, hbond3;")
cmd.do("color gray70, hbond4;")
cmd.do("show nb_spheres;")
cmd.do("set nb_spheres_size, 0.35;")
cmd.do("hide labels;")
cmd.do("ray 1600,1000;")
cmd.do("png ${1:4PCO}.png")
$0
snippet bu
abbr bu
alias bu
cmd.do("run ~/${1:Scripts/PyMOLScripts}/quat.py;")
cmd.do("quat;")
$0
snippet doubleBond
abbr doubleBond
alias doubleBond
cmd.do("set valence, 1; ")
cmd.do("set valence_mode, 1;")
$0
snippet cblind
abbr cblind
alias cblind
cmd.do("run ~/${1:Pymol-script-repo}/colorblindfriendly.py;")
cmd.do("as cartoon;")
cmd.do("color cb_red, ss H;")
cmd.do("color cb_yellow,ss S;")
cmd.do("color cb_green, ss L+;")
$0
snippet centerpi
abbr centerpi
alias centerpi
cmd.do("pseudoatom pi_cent,/${1:3nd3}/${2:A}/${3:U`15}/cg+cz;")
cmd.do("dist pi_cent////ps1, b/${4:U`15}/${5:aaa};")
$0
snippet cribbon
abbr cribbon
alias cribbon
cmd.do("as cartoon;")
cmd.do("color red, ss H;")
cmd.do("color yellow,ss S;")
cmd.do("color green, ss L+;")
$0
snippet cspheres
abbr cspheres
alias cspheres
cmd.do("as spheres;")
cmd.do("color gray30, chain ${1:A};")
cmd.do("color white, chain ${2:B};")
cmd.do("color green, name CL;")
cmd.do("color brown, resn NAG;")
cmd.do("color red, resi 381;")
cmd.do("remove solvent;")
cmd.do("set specular, 0;")
cmd.do("set ray_trace_gain, 0;")
cmd.do("set ray_trace_mode, 3;")
cmd.do("bg_color white;")
cmd.do("set ray_trace_color, black;")
cmd.do("set depth_cue,0;")
$0
snippet coordinate
abbr coordinate
alias coordinate
cmd.do("viewport 900,600;")
cmd.do("fetch 3nd4, type=pdb, async=0;")
cmd.do("run ~/Scripts/PyMOLScripts/quat.py;")
cmd.do("quat 3nd4;")
cmd.do("show sticks;")
cmd.do("set stick_radius=0.125;")
cmd.do("hide everything, name H*;")
cmd.do("bg_color white;")
cmd.do("create coorCov, (3nd4_1 and (resi 19 or resi 119 or resi 219 or resi 319 or resi 419 or resi 519 or (resi 3 and name N7)));")
cmd.do("bond (coorCov//A/NA`19/NA),(coorCov//A/A`3/N7);")
cmd.do("bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`119/O);")
cmd.do("bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`219/O);")
cmd.do("bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`319/O);")
cmd.do("bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`519/O);")
cmd.do("distance (3nd4_1 and chain Aand resi 19 and name NA), (3nd4_1 and chain A and resi 519);")
cmd.do("distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 419);")
cmd.do("distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 319);")
cmd.do("distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 219);")
cmd.do("show nb_spheres; ")
cmd.do("set nb_spheres_size, .35;")
cmd.do("distance hbond1,/3nd4_1/1/A/HOH`119/O, /3nd4_1/1/A/A`3/OP2;")
cmd.do("distance hbond2,/3nd4_1/1/A/HOH`319/O, /3nd4_1/1/A/A`3/OP2;")
cmd.do("distance hbond3,/3nd4_1/1/A/HOH`91/O,/3nd4_1/1/A/HOH`119/O;")
cmd.do("distance hbond4,/3nd4_1/1/A/G`4/N7,/3nd4_1/1/A/HOH`91/O;")
cmd.do("distance hbond5,/3nd4_1/1/A/G`4/O6, /3nd4_1/1/A/HOH`419/O;")
cmd.do("distance hbond6,/3nd4_1/1/A/HOH`91/O,/3nd4_1/1/A/G`4/OP2;")
cmd.do("distance hbond7,/3nd4_1/1/A/HOH`319/O,/3nd4_1/1/A/G`2/OP2;")
cmd.do("distance hbond9,/3nd4_1/1/A/HOH`419/O,/3nd4_2/2/A/HOH`74/O;")
cmd.do("distance hbond10,/3nd4_2/2/A/C`15/O2,/3nd4_1/1/A/G`2/N2;")
cmd.do("distance hbond11, /3nd4_2/2/A/C`15/N3,/3nd4_1/1/A/G`2/N1;")
cmd.do("distance hbond12,/3nd4_2/2/A/C`15/N4,/3nd4_1/1/A/G`2/O6;")
cmd.do("distance hbond13, /3nd4_2/2/A/U`14/N3,/3nd4_1/1/A/A`3/N1;")
cmd.do("distance hbond14,3nd4_2/2/A/U`14/O4,/3nd4_1/1/A/A`3/N6;")
cmd.do("distance hbond15, /3nd4_2/2/A/C`13/N4,/3nd4_1/1/A/G`4/O6;")
cmd.do(" distance hbond16,/3nd4_2/2/A/C`13/N3, /3nd4_1/1/A/G`4/N1;")
cmd.do("distance hbond17, /3nd4_1/1/A/G`4/N2,/3nd4_2/2/A/C`13/O2;")
cmd.do("distance hbond18,/3nd4_1/1/A/G`2/N2,/3nd4_2/2/A/C`15/O2;")
cmd.do("distance hbond19,/3nd4_1/1/A/HOH`91/O,/3nd4_1/1/A/G`4/OP2; ")
cmd.do("set depth_cue=0;")
cmd.do("set ray_trace_fog=0;")
cmd.do("set dash_color, black;")
cmd.do("set label_font_id, 5;")
cmd.do("set label_size, 36;")
cmd.do("set label_position, (0.5, 1.0, 2.0);")
cmd.do("set label_color, black;")
cmd.do("set dash_gap, 0.2;")
cmd.do("set dash_width, 2.0;")
cmd.do("set dash_length, 0.2;")
cmd.do("set label_color, black;")
cmd.do("set dash_gap, 0.2;")
cmd.do("set dash_width, 2.0;")
cmd.do("set dash_length, 0.2;")
cmd.do("select carbon, element C;")
cmd.do("color yellow, carbon;")
cmd.do("disable carbon;")
cmd.do("set_view(-0.9,0.34,-0.26,0.33,0.18,-0.93,-0.27,-0.92,-0.28,-0.07,-0.23,-27.83,8.63,19.85,13.2,16.0,31.63,-20.0)")
$0
snippet distance
abbr distance
alias distance
cmd.do("# Edit the name for the ditance, the selection criteria for atom 1, and the selection criteria for atom 2.;")
cmd.do("distance ${1:dist3}, ${2:/rcsb074137//B/IOD`605/I`B}, ${3:/rcsb074137//B/IOD`605/I`A};")
$0
snippet drawHbonds
abbr drawHbonds
alias drawHbonds
cmd.do("hide everything, hydrogens;")
cmd.do("hide labels;")
cmd.do("# set the color of the dashed lines representing the H-bond.;")
cmd.do("set dash_color, ${1:black};")
cmd.do("set dash_gap, 0.4;")
cmd.do("set dash_radius, 0.08;")
$0
snippet carvedIsomesh
abbr carvedIsomesh
alias carvedIsomesh
cmd.do("delete all;")
cmd.do("# Fetch the coordinates. Need internet connection.")
cmd.do("fetch ${1:4dgr}, async=0;")
cmd.do("# Fetch the electron density map.")
cmd.do("fetch ${1:4dgr}, type=2fofc,async=0;")
cmd.do("# create a selection out of the glycan")
cmd.do("select ${2:LongGlycan}, resi ${3:469:477};")
cmd.do("orient ${2:LongGlycan};")
cmd.do("remove not ${2:LongGlycan};")
cmd.do("remove name H*;")
cmd.do("isomesh 2fofcmap, ${1:4dgr}_2fofc, 1, ${2:LongGlycan}, carve = 1.8;")
cmd.do("color density, 2fofcmap; ")
cmd.do("show sticks;")
cmd.do("show spheres;")
cmd.do("set stick_radius, .07;")
cmd.do("set sphere_scale, .19;")
cmd.do("set sphere_scale, .13, elem H;")
cmd.do("set bg_rgb=[1, 1, 1];")
cmd.do("set stick_quality, 50;")
cmd.do("set sphere_quality, 4;")
cmd.do("color gray85, elem C;")
cmd.do("color red, elem O;")
cmd.do("color slate, elem N;")
cmd.do("color gray98, elem H;")
cmd.do("set stick_color, gray50;")
cmd.do("set ray_trace_mode, 1;")
cmd.do("set ray_texture, 2;")
cmd.do("set antialias, 3;")
cmd.do("set ambient, 0.5;")
cmd.do("set spec_count, 5;")
cmd.do("set shininess, 50;")
cmd.do("set specular, 1;")
cmd.do("set reflect, .1;")
cmd.do("set dash_gap, 0;")
cmd.do("set dash_color, black;")
cmd.do("set dash_gap, .15;")
cmd.do("set dash_length, .05;")
cmd.do("set dash_round_ends, 0;")
cmd.do("set dash_radius, .05;")
cmd.do("set_view (0.34,-0.72,0.61,0.8,0.56,0.22,-0.51,0.4,0.77,0.0,0.0,-81.31,44.64,-9.02,58.62,65.34,97.28,-20.0);")
cmd.do("preset.ball_and_stick(\"all\",mode=1);")
cmd.do("draw;")
$0
snippet fetch2FoFcIsomesh
abbr fetch2FoFcIsomesh
alias fetch2FoFcIsomesh
cmd.do("fetch ${1:3nd4}, ${1:3nd4}_2fofc, type=2fofc, async=0;")
cmd.do("isomesh 2fofcmap, ${1:3nd4}_2fofc, 1, ${1:3nd4}, carve = 1.8;")
$0
snippet fetchCIF
abbr fetchCIF
alias fetchCIF
cmd.do("fetch ${1:3nd4}, type=cif, async=0;")
$0
snippet fetchFoFc
abbr fetchFoFc
alias fetchFoFc
cmd.do("fetch ${1:3nd4}, ${1:3nd4}_fofc, type=fofc, async=0;")
$0
snippet filledRing
abbr filledRing
alias filledRing
cmd.do("show sticks;set cartoon_ring_mode, 3;")
cmd.do("set cartoon_ring_finder, 1;")
cmd.do("set cartoon_ladder_mode, 1;")
cmd.do("set cartoon_nucleic_acid_mode, 4;")
cmd.do("set cartoon_ring_transparency, 0.5;")
cmd.do("as cartoon;")
$0
snippet hbonddash
abbr hbonddash
alias hbonddash
cmd.do("hide everything, hydrogens;")
cmd.do("hide labels;")
cmd.do("set dash_color, black; ")
cmd.do("set dash_gap, 0.4;")
cmd.do("set dash_radius, 0.08;")
$0
snippet hidealtloc
abbr hidealtloc
alias hidealtloc
cmd.do("select altconf, alt ${1:b} # select B alternative locators;")
cmd.do("hide everything, altconf # hide alt B locators;")
$0
snippet labelResnResi
abbr labelResnResi
alias labelResnResi
cmd.do("label name ca, \"%s%s\" %(one_letter[${1:resn}],${2:resi});")
$0
snippet labelSS
abbr labelSS
alias labelSS
cmd.do("alter ${1:chain A}, ss=\"${2:helix}\";")
cmd.do("label (%2),\"%3\";")
$0
snippet loadPDBbs
abbr loadPDBbs
alias loadPDBbs
cmd.do("fetch ${1:3nd3},name=${1:3nd3}, type=pdb, async=0;")
cmd.do("hide (name H*);")
cmd.do("hide lines;")
cmd.do("show sticks;")
cmd.do("set stick_radius, ${2:1.2};")
cmd.do("set nb_sphere_radius, ${3:0.35};")
cmd.do("orient;")
$0
snippet loadPDBnb
abbr loadPDBnb
alias loadPDBnb
cmd.do("fetch ${1:3nd3}, name=${1:3nd3}, type=pdb, async=0;")
cmd.do("orient;")
cmd.do("set stick_radius, ${2:1.2};")
cmd.do("hide (name H*);")
cmd.do("set nb_sphere_size, ${3:0.35};")
cmd.do("set nb_spheres_quality, ${4:1};")
cmd.do("show nb_spheres;")
$0
snippet ms
abbr ms
alias ms
cmd.do("fetch ${1:3nd3}, name=${1:3nd3}, type=pdb, async=0;")
cmd.do("select ${2:temp}, ${1:3nd3} and chain ${4:A};")
cmd.do("run ${5:/Users/blaine-mooers/Scripts/PyMOLScripts/msms_pymol.py};")
cmd.do("calc_msms_area ${2:temp};")
$0
snippet molscriptRibbon
abbr molscriptRibbon
alias molscriptRibbon
cmd.do("set cartoon_highlight_color, grey;")
cmd.do("show cartoon;")
cmd.do("set cartoon_flat_sheets, 0;")
cmd.do("set cartoon_smooth_loops, 0;")
cmd.do("set cartoon_fancy_helices, 1;")
$0
snippet oneLetter
abbr oneLetter
alias oneLetter
cmd.do("one_leVer%={\"VAL\":\"V\",%\"ILE\":\"I\",%\"LEU\":\"L\",%\"GLU\":\"E\",%\"GLN\":\"Q\",\"ASP\":\"D\",%\"ASN\":\"N\",%\"HIS\":\"H\",%\"TRP\":\"W\",%\"PHE\":\"F\",%\"TYR\":\"Y\",%\"ARG\":\"R\",%\"LYS\":\"K\",%\"SER\":\"S\",%\"THR\":\"T\",%\"MET\":\"M\",%\"ALA\":\"A\",%\"GLY\":\"G\",%\"PRO\":\"P\",%\"CYS\":\"C\"}%")
$0
snippet pseudolabel
abbr pseudolabel
alias pseudolabel
cmd.do("pseudoatom ${1:forLabel};")
cmd.do("label ${1:forLabel}, \"%0\";")
cmd.do("set label_color, ${2:red};")
$0
snippet rotate
abbr rotate
alias rotate
cmd.do("rotate ${1:x}, ${2:45}, ${3:pept};")
$0
snippet stereoDraw
abbr stereoDraw
alias stereoDraw
cmd.do("stereo walleye; ")
cmd.do("set ray_shadow, off; ")
cmd.do("#draw 3200,2000;")
cmd.do("draw ${1:1600,1000}; ")
cmd.do("png ${2:aaa}.png;")
$0
snippet stereoRay
abbr stereoRay
alias stereoRay
cmd.do("stereo; ")
cmd.do("set ray_shadow, off;")
cmd.do("ray ${1:2400,1200};")
cmd.do("png ${2:aaa}.png;")
$0
snippet loadThreeMaps
abbr loadThreeMaps
alias loadThreeMaps
cmd.do("load ${1:4dgr}.pdb;")
cmd.do("# Make sure to rename map file so that;")
cmd.do("# the root filename differs from pdb root filename;")
cmd.do("load ${1:4dgr}_2fofc.ccp4, 2fofc;")
cmd.do("load ${1:4dgr}_fofc.ccp4, fofc;")
cmd.do("select ${2:glycan}, resid 200 or (resid 469:477);")
cmd.do("isomesh ${3:mesh1}, 2fofc, 1.0, ${2:glycan};")
cmd.do("color density, ${3:mesh1};")
cmd.do("isomesh ${4:mesh2}, fofc, 3.0, ${2:glycan};")
cmd.do("color green, ${4:mesh2};")
cmd.do("isomesh ${5:mesh3}, fofc, -3.0, ${2:glycan};")
cmd.do("color red, ${5:mesh3};")
$0
snippet turnAboutAxis
abbr turnAboutAxis
alias turnAboutAxis
cmd.do("turn ${1:x},${2:90};")
$0
snippet volumeRamp
abbr volumeRamp
alias volumeRamp
cmd.volume_ramp_new("ramp_magenta", [0.01, 1.00, 0.00, 1.00, 0.00, 4.01, 1.00, 0.00, 1.00, 0.10, 4.99, 1.00, 0.00, 1.00, 0.50,]) $0
$0
snippet solventRadius
abbr solventRadius
alias solventRadius
cmd.do("set solvent_radius, ${1:1.55};")
$0
snippet rv
abbr rv
alias rv
cmd.do("run roundview.py;")
$0
snippet spse
abbr spse
alias spse
cmd.do("python;")
cmd.do("import datetime;")
cmd.do("from pymol import cmd; ")
cmd.do("DT =datetime.datetime.now().strftime(\"yr%Ymo%mday%dhr%Hmin%M\");")
cmd.do("s = str(DT); ")
cmd.do("cmd.save(stemName+s+\".pse\"); ")
cmd.do("python end;")
$0
snippet sc222
abbr sc222
alias sc222
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 2, 2, 2, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet pearl
abbr pearl
alias pearl
cmd.do("create ${1:sodium2}, ${2:sodium1};")
cmd.do("set sphere_transparency, 0.4, ${1:sodium2};")
cmd.do("set sphere_scale, 1.05, ${1:sodium2};")
cmd.do("ray;")
$0
snippet fog
abbr fog
alias fog
cmd.do("set fog, 0;")
$0
snippet rmwater
abbr rmwater
alias rmwater
cmd.do("remove resn HOH;")
$0
snippet setcolor
abbr setcolor
alias setcolor
cmd.do("set_color ${1:bark}, [${2:0.1, ${3:0.1}, ${4:0.1}];")
cmd.do("color ${1:bark}, ${5:protein};")
$0
snippet duplicateObject
abbr duplicateObject
alias duplicateObject
cmd.do("create ${1:t4l}, ${2:1lw9};")
$0
snippet selectChain
abbr selectChain
alias selectChain
cmd.do("select ${1:rna}, ${2:chain B};")
$0
snippet selectResidues
abbr selectResidues
alias selectResidues
cmd.do("select aromatic, resn phe+tyr+trp;")
$0
snippet selectResi
abbr selectResi
alias selectResi
cmd.do("select ${!:se}; resi ${2: 1:100};")
$0
snippet selectElement
abbr selectElement
alias selectElement
cmd.do("select ${1:oxygen}, elem ${2:O};")
$0
snippet selectName
abbr selectName
alias selectName
cmd.do("select ${1:oxygen2}, name ${2:O2};")
$0
snippet selectHelices
abbr selectHelices
alias selectHelices
cmd.do("select ${1:helices}, ss h; ")
$0
snippet selectStrands
abbr selectStrands
alias selectStrands
cmd.do("select ${1:strands}, ss s; ")
$0
snippet selectLoops
abbr selectLoops
alias selectLoops
cmd.do("select ${1:loops}, ss l;")
$0
snippet selectAllBut
abbr selectAllBut
alias selectAllBut
cmd.do("select ${1:select1}, elem ${2:N} and chain ${3:A} and not resn ${4:LYS};")
$0
snippet selectAtomsAround
abbr selectAtomsAround
alias selectAtomsAround
cmd.do("select ${1:nearby}, resn ${2:drug} around ${3:5};")
$0
snippet selectResiduesAround
abbr selectResiduesAround
alias selectResiduesAround
cmd.do("select ${1:nearby}, br. resn ${2:drug} around ${3:5};")
$0
snippet undoSelection
abbr undoSelection
alias undoSelection
cmd.do("disable ${1:sele}; ")
$0
snippet loadPDBfile
abbr loadPDBfile
alias loadPDBfile
cmd.do("load ${1:my}.pdb;")
$0
snippet savePNG
abbr savePNG
alias savePNG
cmd.do("png ${1:saveMe}.png, ${2:1920}, ${3:1920}, ${4:600}, ${5:1};")
$0
snippet ringMode
abbr ringMode
alias ringMode
cmd.do("show cartoon, ${1:rna}; set cartoon_ring_mode, ${2:3};")
$0
snippet sidehChainHelper
abbr sidehChainHelper
alias sidehChainHelper
cmd.do("set cartoon_side_chain_helper, on;")
$0
snippet extractPartObj
abbr extractPartObj
alias extractPartObj
cmd.do("extract new_obj, chain A;")
$0
snippet puttyCartoon
abbr puttyCartoon
alias puttyCartoon
cmd.do("show cartoon;")
cmd.do("cartoon putty;")
cmd.do("set cartoon_smooth_loops, 0;")
cmd.do("set cartoon_flat_sheets, 0;")
cmd.do("set cartoon_smooth_loops,0;")
cmd.do("## unset cartoon_smooth_loops;")
$0
snippet hideSelection
abbr hideSelection
alias hideSelection
cmd.do("indicate none")
$0
snippet discreteCartoonColoring
abbr discreteCartoonColoring
alias discreteCartoonColoring
cmd.do("set cartoon_discrete_colors, on;")
$0
snippet sc111
abbr sc111
alias sc111
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 1, 1, 1, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet saxsEnvelope
abbr saxsEnvelope
alias saxsEnvelope
cmd.do("alter ${1:refine_A_Ave_SM_015_0_370-374-0r}, vdw=3.0;")
cmd.do("set solvent_radius = 3.0;")
$0
snippet setpath
abbr setpath
alias setpath
os.environ["PATH"] += os.pathsep +${1: "~/ATSAS-3.0.3-1/bin"}; $0
$0
snippet fetchPath
abbr fetchPath
alias fetchPath
cmd.do("set fetch_path, ${1:/Users/blaine/pdbFiles};")
$0
snippet antialias
abbr antialias
alias antialias
cmd.do("set antialias, 1;")
$0
snippet sigDigits
abbr sigDigits
alias sigDigits
cmd.do("set label_distance_digits, ${1:2};")
cmd.do("set label_angle_digits, ${2:2};")
$0
snippet labelCAs
abbr labelCAs
alias labelCAs
cmd.do("label name CA,\"%s%s\" % (resn,resi);")
$0
snippet labelWatersHOH
abbr labelWatersHOH
alias labelWatersHOH
cmd.do("label resn HOH ,\"%s%s\" % (resn,resi);")
$0
snippet labelWatersW
abbr labelWatersW
alias labelWatersW
cmd.do("label resn HOH ,\"W%s\" % (resi);")
$0
snippet findHbonds
abbr findHbonds
alias findHbonds
cmd.do("remove element h; distance hbonds, all, all, 3.2, mode=2;")
$0
snippet printBs
abbr printBs
alias printBs
cmd.do("remove element h; iterate resi ${1: 1:13}, print(resi, name,b);")
$0
snippet labelMainChain
abbr labelMainChain
alias labelMainChain
cmd.do("label name n+c+o+ca,\"%s%s%s\" % (resn,resi,name);")
$0
snippet printBspartB
abbr printBspartB
alias printBspartB
cmd.do("iterate resi ${1:38} and altloc ${2:B}, print resi, name, alt, b;")
$0
snippet printBs2digits
abbr printBs2digits
alias printBs2digits
cmd.do("iterate (resi ${1:133}), print(name + \" %.2f\" % b);")
$0
snippet writeCommandReference2HTML
abbr writeCommandReference2HTML
alias writeCommandReference2HTML
cmd.write_html_ref("pymol-command-ref.html"); $0
$0
snippet averageB
abbr averageB
alias averageB
cmd.do("Bfactors = []; ")
cmd.do("# >>> edit the selection below, which is a range of residue numbers here.;")
cmd.do("iterate (resi ${1:133}), Bfactors.append(b);")
cmd.do("print(\"Sum = \", \"%.2f\" % (sum(Bfactors)));")
cmd.do("print(\"Number of atoms = \", len(Bfactors));")
cmd.do("print( \"Average B =\" , \"%.2f\" % ( sum(Bfactors)/float(len(Bfactors))));")
$0
snippet printNameB4ResiX
abbr printNameB4ResiX
alias printNameB4ResiX
Bfac_dict = { "Bfactors3" : [] };
cmd.iterate("(${1:resi 133})","Bfactors3.append((name, b))", space=Bfac_dict);
[print("%s %.2f" % (i,j)) for i,j in Bfac_dict["Bfactors3"]; $0
$0
snippet printResiResnNameB4ResiX
abbr printResiResnNameB4ResiX
alias printResiResnNameB4ResiX
Bfac_dict = { "Bfactors3" : [] };
cmd.iterate("(${1:resi 133})","Bfactors3.append((resn,resi,name, b))", space=Bfac_dict);
[print("%s %s %s %.2f" % (i,j,k,l)) for i,j,k,l in Bfac_dict["Bfactors3"]] $0
$0
snippet printResiResnNameB4ResiXNoH
abbr printResiResnNameB4ResiXNoH
alias printResiResnNameB4ResiXNoH
Bfac_dict = { "Bfactors3" : [] };
cmd.iterate("(${1:resi 133} and not elem H)","Bfactors3.append((resn,resi,name, b))", space=Bfac_dict);
[print("%s %s %s %.2f" % (i,j,k,l))for i,j,k,l in Bfac_dict["Bfactors3"]]; $0
$0
snippet internalGUImode2
abbr internalGUImode2
alias internalGUImode2
cmd.do("internal_gui_mode=2;")
$0
snippet internalGUIwidth
abbr internalGUIwidth
alias internalGUIwidth
cmd.do("set internal_gui_width=${1:0};")
$0
snippet printDoc
abbr printDoc
alias printDoc
print(${1:my_func}.__doc__); $0
$0
snippet his31asp70
abbr his31asp70
alias his31asp70
cmd.do("fetch ${1:1lw9}, async=0; ")
cmd.do("zoom (${2:resi 31 or resi 70}); ")
cmd.do("preset.technical(selection=\"all\"); ")
cmd.do("bg_color ${3:gray70}; ")
cmd.do("clip slab, 7,(${4:resi 31 or resi 70});")
cmd.do("rock;")
$0
snippet waterTriple
abbr waterTriple
alias waterTriple
cmd.do("fetch ${1:lw9}, async=0; ")
cmd.do("zoom resi ${2:313}; ")
cmd.do("preset.technical(selection=\"all\", mode=1);")
$0
snippet ligandSelect
abbr ligandSelect
alias ligandSelect
cmd.do("select ${1:ligand}, organic;")
$0
snippet github
abbr github
alias github
cmd.do("https://github.com/MooersLab/pymolsnips/blob/master/README.md")
$0
snippet sigdihedral
abbr sigdihedral
alias sigdihedral
cmd.do("set label_dihedral_digits, ${1:2};")
$0
snippet stateOne
abbr stateOne
alias stateOne
cmd.create("newobject", "oldobject", "1", "1"); $0
$0
snippet sc112
abbr sc112
alias sc112
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 1, 1, 2, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet sc113
abbr sc113
alias sc113
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 1, 1, 3, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet sc311
abbr sc311
alias sc311
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 3, 1, 1, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet sc131
abbr sc131
alias sc131
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 1, 3, 1, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet sc211
abbr sc211
alias sc211
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 2, 1, 1, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet sc121
abbr sc121
alias sc121
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 1, 2, 1, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet sc122
abbr sc122
alias sc122
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 1, 2, 2, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet sc221
abbr sc221
alias sc221
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 2, 2, 1, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet sc212
abbr sc212
alias sc212
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 2, 1, 2, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet sc133
abbr sc133
alias sc133
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 1, 3, 3, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet sc313
abbr sc313
alias sc313
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 3, 1, 3, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet sc331
abbr sc331
alias sc331
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 3, 3, 1, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet sc233
abbr sc233
alias sc233
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 2, 3, 3, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet sc323
abbr sc323
alias sc323
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 1, 1, 1, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet sc332
abbr sc332
alias sc332
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 3, 3, 2, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet sc333
abbr sc333
alias sc333
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 3, 3, 3, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet sc114
abbr sc114
alias sc114
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 1, 1, 4, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet sc141
abbr sc141
alias sc141
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 1, 4, 1, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet sc411
abbr sc411
alias sc411
cmd.do("run $HOME/${1:Scripts/PyMOLscripts/}supercell.py;")
cmd.do("supercell 4, 1, 1, , ${2:orange}, ${3:supercell1}, 1;")
$0
snippet sccp4
abbr sccp4
alias sccp4
cmd.do("python;")
cmd.do("import datetime;")
cmd.do("from pymol import cmd; ")
cmd.do("DT =datetime.datetime.now().strftime(\"yr%Ymo%mday%dhr%Hmin%M\");")
cmd.do("s = str(DT); ")
cmd.do("cmd.save(stemName+s+\".ccp4\"); ")
cmd.do("python end;")
$0
snippet sdae
abbr sdae
alias sdae
import datetime;
DT =datetime.datetime.now().strftime("yr%Ymo%mday%dhr%Hmin%M");
s = str(DT);
cmd.save(stemName+s+".dae");
$0
snippet carvedIsosurface
abbr carvedIsosurface
alias carvedIsosurface
cmd.do("delete all;")
cmd.do("# Fetch the coordinates. Need internet connection.;")