/usr/share/doc/raster3d/examples/example3.mol is in raster3d-doc 3.0-3-2.
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 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 | ! MOLSCRIPT V1.4 description file for LT/gal
! galactose binding site, showing 1 complete monomer
! color version with individually labeled residues
!
plot
area 50. 100. 575. 650. ;
background black ;
window 35.0 ;
!
! All non-hydrogen atoms
!
read LT "LT.pdb" ;
transform atom *
by centre position require in residue G104 and atom C3
by rotation z -90.0
by rotation y -110.0
by rotation z -30.0
by rotation x 8.0
by translation -4.0 0. 0.
by rotation y 2.0
;
!
! Increase the number of segments to get smoother shading
!
set segments 10 ;
!
! B5 pentamer
!
set planecolour hsb 0.15 1.0 1.0 ;
set plane2colour hsb 0.15 1.0 0.6 ;
set linecolour hsb 0.15 1.0 0.3 ;
turn from F1 to F5 ;
helix from F5 to F9 ; coil from F9 to F15 ;
strand from F15 to F22 ; coil from F22 to F26 ;
strand from F26 to F30 ; coil from F30 to F37 ;
strand from F37 to F41 ; coil from F41 to F47 ;
strand from F47 to F50 ; coil from F50 to F59 ;
helix from F59 to F77 ; coil from F77 to F82 ;
strand from F82 to F88 ; coil from F88 to F94 ;
strand from F94 to F102; turn from F102 to F103 ;
set planecolour hsb 0.27 0.6 1.0 ;
set plane2colour hsb 0.27 0.8 0.6 ;
set linecolour hsb 0.27 1.0 0.3 ;
turn from G1 to G5 ;
helix from G5 to G9 ; coil from G9 to G15 ;
strand from G15 to G22 ; coil from G22 to G26 ;
strand from G26 to G30 ; coil from G30 to G37 ;
strand from G37 to G41 ; coil from G41 to G47 ;
strand from G47 to G50 ; coil from G50 to G59 ;
helix from G59 to G77 ; coil from G77 to G82 ;
strand from G82 to G88 ; coil from G88 to G94 ;
strand from G94 to G102; turn from G102 to G103 ;
set planecolour hsb 0.52 0.8 1.0 ;
set plane2colour hsb 0.52 0.9 0.6 ;
set linecolour hsb 0.52 1.0 0.3 ;
turn from H1 to H5 ;
helix from H5 to H9 ; coil from H9 to H15 ;
strand from H15 to H22 ; coil from H22 to H26 ;
strand from H26 to H30 ; coil from H30 to H37 ;
strand from H37 to H41 ; coil from H41 to H47 ;
strand from H47 to H50 ; coil from H50 to H59 ;
helix from H59 to H77 ; coil from H77 to H82 ;
strand from H82 to H88 ; coil from H88 to H94 ;
strand from H94 to H102; turn from H102 to H103 ;
! Solvents
set atomcolour atom OH2 hsb 0.75 0.3 0.7 ;
set atomradius atom OH2 0.5 ;
cpk require atom OH2 and sphere position in residue G88 9.0 ;
set labelcentre on ;
set labelclip off ;
set labelsize 12. ;
set depthcue 0.4 ;
set labeloffset 0.0 0.0 0.5 ;
set linecolour white ;
label require atom OH2 and in residue W270 "1" ;
label require atom OH2 and in residue W147 "2" ;
label require atom OH2 and in residue W295 "3" ;
label require atom OH2 and in residue W292 "4" ;
label require atom OH2 and in residue W153 "5" ;
label require atom OH2 and in residue W294 "6" ;
! sugar molecule
set atomradius atom * 0.6 ;
set atomradius atom C* 0.01 ;
set atomcolour atom C* grey 0.5 ;
! emphasize oxygens
set atomradius atom O* 0.6 ;
set atomcolour atom O* hsb 0.00 0.5 0.9 ;
! ditto for nitrogens
set atomradius atom N* 0.6 ;
set atomcolour atom N* hsb 0.66 0.5 0.9 ;
set stickradius 0.1 ;
set sticktaper 0.0 ;
set planecolour hsb 0.05 0.8 0.9 ;
set plane2colour hsb 0.05 0.8 0.9 ;
set linecolour hsb 0.05 0.8 0.9 ;
ball-and-stick in residue G104 ;
! Nearby residues in protein
set planecolour grey 0.8 ;
set plane2colour grey 0.8 ;
set linecolour grey 0.0 ;
set atomcolour atom C* grey 0.8 ;
set stickradius 0.1 ;
set sticktaper 0.0 ;
ball-and-stick
either
in from G12 to G14,
in residue G51,
in from G56 to G57,
in residue G61,
in from G88 to G91
or in residue H33
;
!
! Labels
!
set labelcentre off ;
set labelclip on ;
set labelsize 12. ;
set depthcue 0.4 ;
set linecolour white ;
set labeloffset -3.0 0.5 0.5 ;
label require atom CA and in residue G13 "Arg 13" ;
set labeloffset -1.3 -1.2 0.5 ;
label require atom CZ2 and in residue G88 "Trp 88" ;
set labeloffset -4.5 0.5 0.5 ;
label require atom CA and in residue G14 "Asn 14" ;
set labeloffset 0.5 0.0 0.5 ;
label require atom OE1 and in residue G56 "Gln 56" ;
set labeloffset -3.2 -0.1 0.5 ;
label require atom CA and in residue H33 "Gly 33*" ;
set labeloffset -2.5 5.5 0.5 ;
label require atom OD1 and in residue G90 "Asn 90" ;
set labeloffset 2.0 0.0 0.5 ;
label require atom CB and in residue G51 "Glu 51" ;
set labeloffset 0.5 -0.5 0.5 ;
label require atom N and in residue G61 "Gln 61" ;
set labeloffset -1.6 4.2 0.5 ;
label require atom CB and in residue G91 "Lys 91" ;
set labeloffset -1.0 -1.5 0.5 ;
label require atom CA and in residue G12 "Tyr 12" ;
set labeloffset 0.5 1.0 0.5 ;
label require atom CB and in residue G57 "His 57" ;
end_plot
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