Coords_DF_handout

Coords_DF_handout - 1 From Molecules to Simulations...

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Unformatted text preview: 1 From Molecules to Simulations: Coordinate Systems and Conformational Space BIOL 7110 / CHEM 8901 / BIOL 4105 / CHEM 4804 February 8, 2011 Two Principal Coordinate Systems in Macromolecular Modeling Cartesian coordinates : x,y,z coordinates of each atom Internal coordinates : Values of bond lengths bond angles and torsion angles 2 Atomic Cartesian Coordinates are Given in a PDB File ( P rotein D ata B ank) HEADER HYDROLASE (O-GLYCOSYL) 01-SEP-95 193L TITLE THE 1.33 A STRUCTURE OF TETRAGONAL HEN EGG WHITE LYSOZYME ATOM 1 N LYS 1 3.336 10.074 10.331 ATOM 2 CA LYS 1 2.429 10.424 9.199 ATOM 3 C LYS 1 2.415 11.932 8.954 ATOM 4 O LYS 1 2.390 12.719 9.904 . . . ATOM 1012 OXT LEU 129 -17.780 19.420 8.236 TER 1013 LEU 129 x (Å) y (Å) z(Å) The molecular conformation is specified by a 3N-dimensional vector R = (x 1 , y 1 , z 1 , x 2 , y 2 , z 2 , . . . , x N , y N , z N ) Extract from a PDB file HEADER HYDROLASE (O-GLYCOSYL) 01-SEP-95 193L TITLE THE 1.33 A STRUCTURE OF TETRAGONAL HEN EGG WHITE LYSOZYME . . . ATOM 1 N LYS 1 3.336 10.074 10.331 1.00 13.37 193L ATOM 2 CA LYS 1 2.429 10.424 9.199 1.00 14.29 193L ATOM 3 C LYS 1 2.415 11.932 8.954 1.00 14.29 193L ATOM 4 O LYS 1 2.390 12.719 9.904 1.00 13.66 193L ATOM 5 CB LYS 1 1.000 9.944 9.506 1.00 15.13 193L ATOM 6 CG LYS 1 -0.038 10.444 8.543 1.00 16.82 193L ATOM 7 CD ALYS 1 -1.418 9.911 8.867 0.45 17.79 193L ATOM 8 CD BLYS 1 -1.427 9.945 8.931 0.55 17.16 193L ATOM 9 CE ALYS 1 -2.457 10.562 7.967 0.45 18.84 193L ATOM 10 CE BLYS 1 -2.516 10.672 8.152 0.55 18.12 193L ATOM 11 NZ ALYS 1 -3.794 9.917 8.074 0.45 18.73 193L ATOM 12 NZ BLYS 1 -2.434 10.503 6.669 0.55 17.26 193L ATOM 13 N VAL 2 2.467 12.329 7.688 1.00 13.97 193L ATOM 14 CA VAL 2 2.417 13.741 7.336 1.00 14.71 193L . . . ATOM 1001 CZ ARG 128 -15.523 16.242 -0.491 1.00 41.19 193L ATOM 1002 NH1 ARG 128 -16.104 16.952 -1.456 1.00 42.18 193L ATOM 1003 NH2 ARG 128 -14.461 15.491 -0.771 1.00 43.01 193L ATOM 1004 N LEU 129 -15.649 19.796 5.781 1.00 30.47 193L ATOM 1005 CA LEU 129 -15.598 19.391 7.196 1.00 32.89 193L ATOM 1006 C LEU 129 -16.827 18.716 7.823 1.00 34.37 193L ATOM 1007 O LEU 129 -16.795 17.480 7.978 1.00 35.24 193L ATOM 1008 CB LEU 129 -15.170 20.567 8.085 1.00 32.71 193L ATOM 1009 CG LEU 129 -13.704 20.986 8.223 1.00 33.56 193L ATOM 1010 CD1 LEU 129 -12.810 19.776 8.179 1.00 33.22 193L ATOM 1011 CD2 LEU 129 -13.330 21.963 7.147 1.00 35.05 193L ATOM 1012 OXT LEU 129 -17.780 19.420 8.236 1.00 35.18 193L TER 1013 LEU 129 193L HETATM 1014 CL CL 130 -8.209 31.412 26.225 1.00 21.43 193L HETATM 1015 NA NA 131 7.951 14.394 31.641 1.00 20.97 193L HETATM 1016 O HOH 132 13.939 14.955 26.581 1.00 11.46 193L HETATM 1017 O HOH 133 11.588 11.854 32.757 1.00 14.08 193L HETATM 1018 O HOH 134 11.548 13.300 14.902 1.00 11.29 193L ....
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This note was uploaded on 09/22/2011 for the course BIOL 7110 taught by Professor Steveharvey during the Spring '11 term at Georgia Tech.

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Coords_DF_handout - 1 From Molecules to Simulations...

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