#!/usr/local/bin/vmd
# VMD script written by save_state $Revision: 1.2 $
# VMD version: 1.8.2
set viewplist {}
set fixedlist {}
material add None
material change ambient None 0.000000
material change specular None 0.000000
material change diffuse None 0.000000
material change shininess None 0.000000
material change opacity None 0.000000
# Atom selection macros
atomselect macro at {resname ADE A THY T}
atomselect macro acidic {resname ASP GLU}
atomselect macro cyclic {resname HIS PHE PRO TRP TYR}
atomselect macro acyclic {protein and not cyclic}
atomselect macro aliphatic {resname ALA GLY ILE LEU VAL}
atomselect macro alpha {protein and name CA}
atomselect macro amino protein
atomselect macro aromatic {resname HIS PHE TRP TYR}
atomselect macro basic {resname ARG HIS LYS}
atomselect macro bonded {numbonds > 0}
atomselect macro buried {resname ALA LEU VAL ILE PHE CYS MET TRP}
atomselect macro cg {resname CYT C GUA G}
atomselect macro charged {basic or acidic}
atomselect macro hetero {not (protein or nucleic)}
atomselect macro hydrophobic {resname ALA LEU VAL ILE PRO PHE MET TRP}
atomselect macro small {resname ALA GLY SER}
atomselect macro medium {resname VAL THR ASP ASN PRO CYS ASX PCA HYP}
atomselect macro large {protein and not (small or medium)}
atomselect macro neutral {resname VAL PHE GLN TYR HIS CYS MET TRP ASX GLX PCA HYP}
atomselect macro polar {protein and not hydrophobic}
atomselect macro purine {resname ADE A GUA G}
atomselect macro pyrimidine {resname CYT C THY T URI U}
atomselect macro surface {protein and not buried}
atomselect macro lipid {resname DLPE DMPC GPC LPPC PALM PC PGCL POPC POPE}
atomselect macro lipids lipid
atomselect macro ion {name CLA SOD}
atomselect macro ions {name CLA SOD}
atomselect macro sugar {resname AGLC}
atomselect macro solvent {not (protein or sugar or nucleic or lipid)}
atomselect macro carbon {name "C.*" and not ion}
atomselect macro hydrogen {name "[0-9]?H.*"}
atomselect macro nitrogen {name "N.*"}
atomselect macro oxygen {name "O.*"}
atomselect macro sulfur {name "S.*" and not ion}
atomselect macro noh {not hydrogen}
atomselect macro now {not water}
atomselect macro hg {segname "CA_." and resid 3 to 58}
atomselect macro mid {segname "CA_." and resid 62 to 157 294 to 320}
atomselect macro bot {segname "CA_." and resid 163 to 290 322 to 329}
atomselect macro tail {segname "CA_." and resid 323 to 354}
atomselect macro tail_conn {segname "CA_." and resid 328 to 331}
atomselect macro hg_conn {segname "CA_." and resid 57 to 63}
atomselect macro hg_hydrophobic_core {segname "CA_." and resid 52 to 57}
atomselect macro dna {segname "DNA." and resid 4 to 19}
atomselect macro dna_int {segname "DNA." and resid 11 12}
atomselect macro bc {(segname DNA1 DNA3 and resid 4) or (segname DNA2 DNA4 and resid 19)}
atomselect macro hg_ref {name CA and chain A B and resid 3 to 57 and noh}
atomselect macro hg_comp {name CA and segname CA_1 CA_2 and resid 3 to 57 and noh}
atomselect macro dna_ref {nucleic and backbone and resid 6 to 17}
atomselect macro dna_comp {segname DNA1 DNA2 and backbone and resid 6 to 17}
atomselect macro bot_ref {chain A B and resid 163 to 290 322 to 329}
atomselect macro bot_comp {segname CA_1 CA_2 and resid 163 to 290 322 to 329 and not hydrogen}
atomselect macro mid_ref {chain A B and resid 62 to 157 294 to 320}
atomselect macro mid_comp {segname CA_1 CA_2 and resid 62 to 157 294 to 320 and not hydrogen}
atomselect macro hg_conn_ref {name CA and chain A B and resid 57 to 63}
atomselect macro hg_conn_comp {name CA and segname CA_1 CA_2 and resid 57 to 63}
atomselect macro align_helix {segname "CA_." and resid 103 to 118}
atomselect macro ref {name CA and chain A B}
atomselect macro comp {name CA and segname CA_1 CA_2}
atomselect macro efa_ca_c {name CA and chain A B and resid 30 to 300}
atomselect macro efa_ca_r {name CA and segname CA_1 CA_2 and resid 30 to 300}
atomselect macro efa_hg_c {name CA and chain A B and resid 3 to 58}
atomselect macro efa_hg_r {name CA and segname CA_1 CA_2 and resid 3 to 58}
atomselect macro efa_mid_c {name CA and chain A B and resid 62 to 157 294 to 320}
atomselect macro efa_mid_r {name CA and segname CA_1 CA_2 and resid 62 to 157 294 to 320}
atomselect macro efa_mid-all_c {noh  and chain A B and resid 62 to 157 294 to 320}
atomselect macro efa_mid-all_r {noh  and segname CA_1 CA_2 and resid 62 to 157 294 to 320}
atomselect macro lbi_mid_c {name CA and resid 62 to 157 294 to 320}
atomselect macro lbi_mid_r {name CA and resid 62 to 157 294 to 320}
atomselect macro lbi_bot_c {name CA and resid 163 to 290 322 to 329}
atomselect macro lbi_bot_r {name CA and resid 163 to 290 322 to 329}
atomselect macro lbi_c {lbi_mid_c or lbi_bot_c}
atomselect macro lbi_r {lbi_mid_r or lbi_bot_r}
atomselect macro lbg_mid_c {name CA and resid 62 to 157 294 to 320}
atomselect macro lbg_mid_r {name CA and resid 62 to 157 294 to 320}
atomselect macro lbg_bot_c {name CA and resid 163 to 290 322 to 329}
atomselect macro lbg_bot_r {name CA and resid 163 to 290 322 to 329}
atomselect macro lbg_hg_c {name CA and resid 3 to 58}
atomselect macro lbg_hg_r {name CA and resid 3 to 58}
atomselect macro lbg_c {name CA}
atomselect macro lbg_r {name CA}
# Display settings
display eyesep       0.065000
display focallength  2.000000
display height       6.000000
display distance     -2.000000
display projection   Orthographic
display nearclip set 0.010000
display farclip  set 10.000000
display depthcue   off
display cuestart   0.500000
display cueend     10.000000
display cuedensity 0.400000
display cuemode    Exp2
mol new {PDB/1j4n.pdb} type pdb
mol delrep 0 top
mol representation Tube 0.300000 6.000000
mol color Molecule
mol selection {protein}
mol material Opaque
mol addrep top
mol selupdate 0 top 0
mol colupdate 0 top 0
mol scaleminmax top 0 0.000000 0.000000
mol smoothrep top 0 0
mol drawframes top 0 {now}
mol representation Cartoon 2.100000 12.000000 5.000000
mol color Molecule
mol selection {protein}
mol material Opaque
mol addrep top
mol selupdate 1 top 0
mol colupdate 1 top 0
mol scaleminmax top 1 0.000000 0.000000
mol smoothrep top 1 0
mol drawframes top 1 {now}
mol showrep top 1 0
mol representation Tube 0.300000 6.000000
mol color ColorID 1
mol selection {resid 79 to 88 196 to 204}
mol material Opaque
mol addrep top
mol selupdate 2 top 0
mol colupdate 2 top 0
mol scaleminmax top 2 0.000000 0.000000
mol smoothrep top 2 0
mol drawframes top 2 {now}
mol showrep top 2 0
mol representation Tube 0.300000 6.000000
mol color ColorID 7
mol selection {resid 74 to 78 191 to 195}
mol material Opaque
mol addrep top
mol selupdate 3 top 0
mol colupdate 3 top 0
mol scaleminmax top 3 0.000000 0.000000
mol smoothrep top 3 0
mol drawframes top 3 {now}
mol showrep top 3 0
mol representation Licorice 0.300000 8.000000 6.000000
mol color Name
mol selection {resid 78 to 80 194 to 196}
mol material Opaque
mol addrep top
mol selupdate 4 top 0
mol colupdate 4 top 0
mol scaleminmax top 4 0.000000 0.000000
mol smoothrep top 4 0
mol drawframes top 4 {now}
mol showrep top 4 0
mol representation Licorice 0.300000 8.000000 6.000000
mol color Name
mol selection {resname GLU}
mol material Opaque
mol addrep top
mol selupdate 5 top 0
mol colupdate 5 top 0
mol scaleminmax top 5 0.000000 0.000000
mol smoothrep top 5 0
mol drawframes top 5 {now}
mol showrep top 5 0
mol representation VDW 1.000000 8.000000
mol color Name
mol selection {protein}
mol material Opaque
mol addrep top
mol selupdate 6 top 0
mol colupdate 6 top 0
mol scaleminmax top 6 0.000000 0.000000
mol smoothrep top 6 0
mol drawframes top 6 {now}
mol showrep top 6 0
mol representation VDW 1.000000 8.000000
mol color Name
mol selection {water}
mol material Opaque
mol addrep top
mol selupdate 7 top 0
mol colupdate 7 top 0
mol scaleminmax top 7 0.000000 0.000000
mol smoothrep top 7 0
mol drawframes top 7 {now}
mol showrep top 7 0
mol rename top {1j4n.pdb}
set viewpoints([molinfo top]) {{{1.000000 0.000000 0.000000 -33.827682} {0.000000 1.000000 0.000000 -30.454559} {0.000000 0.000000 1.000000 -27.151075} {0.000000 0.000000 0.000000 1.000000}} {{1.000000 0.000000 0.000000 0.000000} {0.000000 0.000000 1.000000 0.000000} {0.000000 -1.000000 0.000000 0.000000} {0.000000 0.000000 0.000000 1.000000}} {{0.033857 0.000000 0.000000 0.000000} {0.000000 0.033857 0.000000 0.000000} {0.000000 0.000000 0.033857 0.000000} {0.000000 0.000000 0.000000 1.000000}} {{1.000000 0.000000 0.000000 0.000000} {0.000000 1.000000 0.000000 0.000000} {0.000000 0.000000 1.000000 0.000000} {0.000000 0.000000 0.000000 1.000000}}}
lappend viewplist [molinfo top]
set topmol [molinfo top]
# done with molecule 0
foreach v $viewplist {
  molinfo $v set {center_matrix rotate_matrix scale_matrix global_matrix} $viewpoints($v)
}
foreach v $fixedlist {
  molinfo $v set fixed 1
}
unset viewplist
unset fixedlist
mol top $topmol
unset topmol
proc vmdrestoremycolors {} {
  color Resname {BNG} gray
  color Resname {HOH} orange
  color Chain {A} blue
  color Chain {X} red
  color Segname {} blue
  color Molecule {0} blue
  color Surface {Grasp} gray
  color Labels {Springs} orange
  color change rgb 0 0.0 0.0 1.0
  color change rgb 2 0.34999999404 0.34999999404 0.34999999404
  color change rgb 3 1.0 0.5 0.0
  color change rgb 4 1.0 1.0 0.0
  color change rgb 5 0.5 0.5 0.20000000298
  color change rgb 6 0.600000023842 0.600000023842 0.600000023842
  color change rgb 7 0.0 1.0 0.0
  color change rgb 9 1.0 0.600000023842 0.600000023842
  color change rgb 11 0.649999976158 0.0 0.649999976158
  color change rgb 12 0.5 0.899999976158 0.40000000596
  color change rgb 13 0.899999976158 0.40000000596 0.699999988079
  color change rgb 14 0.5 0.300000011921 0.0
  color change rgb 15 0.5 0.5 0.75
}
vmdrestoremycolors