ID code: 9ICL, PDE0101 C ********************************************************************* C FREEHEL98.FOR 1 June 1998 C This is the Fortran program code for helix analysis program FREEHELIX. C For operating instructions, see the separate file FREEHEL98.TEX. This C program is radically changed from the earlier NEWHELIX, deleting the C old RADJ and TADJ, and adding the helix-independent parameters VALL C (total bending), VROL (roll), VTIL (tilt), VTWI (twist), VSLI (slide), C VRIS (rise) and VSHF (shift). This program can be used with DNA C helices of any degree of bending. C Richard E. Dickerson, Oxford C ********************************************************************* TITL CELL 1., 1., 1., 90., 90., 90. BRKH FPUN 0 PMIN 0 PMAX 0 BASE 6 HELX RC1' YC1' HELX RN9 YN1 BROL CYLN TRNG END 1 INPUT FRAC.COORDS. X,Y,Z AND ATOM NAME IN FORMAT: (T31,3F8.3,T20,A1,T25,2A1,T14,3A1) WILL READ 240 ATOMS: PRINT FLAG= 0 CELL CONSTANTS A,B,C,ALPHA,BETA,GAMMA ARE: 1.000 1.000 1.000 90.000 90.000 90.000 COORDINATES IN ORTHONORMAL SYSTEM: PRINT FLAG= 0 ************************************** ATOM PAIRS USED TO DETERMINE THE HELIX AXIS ARE: 8 C02C1' 27 A03C1' 27 A03C1' 48 T04C1' 48 T04C1' 68 C05C1' 68 C05C1' 87 T06C1' 87 T06C1' 107 G07C1' 145 A02C1' 126 C01C1' 166 G03C1' 145 A02C1' 188 A04C1' 166 G03C1' 209 T05C1' 188 A04C1' 229 G06C1' 209 T05C1' 9 C02N1 28 A03N9 28 A03N9 49 T04N1 49 T04N1 69 C05N1 69 C05N1 88 T06N1 88 T06N1 108 G07N9 146 A02N9 127 C01N1 167 G03N9 146 A02N9 189 A04N9 167 G03N9 210 T05N1 189 A04N9 230 G06N9 210 T05N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.64738*S + 15.50585 Y = 0.75654*S + -18.21805 Z = 0.09243*S + 40.51260 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.64738*S + 15.50585 Y = 0.75654*S + -18.21804 Z = 0.09243*S + 40.51260 >>>>>> HELIX ROTATION: 32.945 DISPLACEMENT: 3.5597 STATISTICS: OVERALL STANDARD DEV.: 0.9017 SIGMA(X): 1.0749, SIGMA(Y): 1.1020, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.3629, SIGMA(ROTATION): 7.328 THERE ARE 10.93 RESIDUES PER TURN ***************************************************** THE FOLLOWING DIAMOND LIST HAS BEEN OUTPUT ON UNIT: 12 NORMAL END OF JOB: YOU HAVE GIVEN BIRTH TO A HELIX NUMBER BASE PAIRS = 6 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.07166 0.20949 0.97518 94.11 77.91 12.79 -0.12652 0.10254 0.98665 97.27 84.11 9.37 -0.10300 0.03642 0.99401 95.91 87.91 6.27 0.00504 0.00986 0.99994 89.71 89.44 0.63 -0.04063 -0.15293 0.98740 92.33 98.80 9.10 0.15722 -0.11863 0.98041 80.95 96.81 11.36 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.14967 0.07232 0.98609 98.61 85.85 9.57 -0.03353 -0.02929 0.99901 91.92 91.68 2.55 0.12526 -0.11043 0.98596 82.80 96.34 9.61 0.15305 -0.11086 0.98198 81.20 96.36 10.89 0.26698 -0.08132 0.96026 74.52 94.66 16.21 0.00501 0.24991 0.96826 89.71 75.53 14.48 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.10943 0.12241 0.98643 96.28 82.97 9.45 -0.10096 0.01748 0.99474 95.79 89.00 5.88 -0.03433 -0.05973 0.99762 91.97 93.42 3.95 0.09350 -0.07673 0.99266 84.64 94.40 6.95 0.07158 -0.10958 0.99140 85.90 96.29 7.52 0.17405 0.00418 0.98473 79.98 89.76 10.03 1 I= 1 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 2 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 3 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 4 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 5 PS= 90.0000 LS= 90.0000 PL= 90.0000 1 ANGLES BETWEEN NORMAL VECTORS TO BASE PAIRS J= 1 2 3 4 5 6 I= 1 0 6 11 16 16 17 I= 2 6 0 5 12 12 15 I= 3 11 5 0 7 6 12 I= 4 16 12 7 0 2 6 I= 5 16 12 6 2 0 8 I= 6 17 15 12 6 8 0 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 ROLL AND TILT ANGLES STRAND 2 ROLL AND TILT ANGLES TIP INCL ROLL TILT RADJ TADJ TIP INCL ROLL TILT RADJ TADJ -10.99 6.46 6.03 3.35 0.00****** -2.33 9.28 6.05 -6.47 0.00 -0.00 -7.75 5.24 3.86 1.14 0.00 0.00 1.05 2.33 9.16 -4.61 0.00 0.00 -6.01 1.78 6.36 -0.61 0.00****** 9.57 0.90 1.51 -0.50 0.92 0.00 0.29 -0.57 -4.61 8.55 0.00 0.00 8.84 6.32 6.76 -0.21 0.00 0.00 -6.47 6.38 9.01 7.22 0.00 0.00 10.87 11.87 4.31-24.56 1.75 0.00 -1.77 11.22 0.00 0.00 0.00 0.00 12.88 -6.49 0.00 0.00 0.00 0.00 BEST PLANE THROUGH BOTH BASES VALL VTIL VROL VSLI VTWI VRIS VSHF INCL TIP TILT ROLL SLIDE CUP PROP BUCK X DSP Y DSP 6.05 -0.26 6.05 0.70 28.43 3.66 -0.43 7.58 -5.61 -0.28 6.04 0.75 -5.64 -8.67 2.68 -0.43 0.06 5.85 -0.56 5.82 -0.79 37.11 3.29 -0.09 5.25 -2.63 -0.48 5.83 -0.76 2.11 -8.80 -2.96 -0.95 0.74 7.40 -1.34 7.28 -0.14 35.64 3.21 0.11 3.93 0.42 -1.50 7.25 -0.10 7.79 -15.59 -0.85 -0.78 0.26 2.26 1.49 -1.70 -0.07 30.82 3.49 -0.55 4.37 5.39 1.56 -1.64 -0.07 -1.34 -8.56 6.94 -0.33 0.29 8.79 -0.20 8.79 0.79 31.08 3.85 0.70 7.51 0.34 0.09 8.81 0.85 -23.11 -17.37 5.59 -0.60 0.06 - - - - - - - 8.73 4.90 - - - - -15.04 -17.51 0.45 0.42 NOTE: Angles are calculated from 5" end to 3" end of strand 1, and signs of angles also are calculated with respect to strand 1. To examine individual strand 2 bases w.r.t. strand 2, reverse signs of Tip and Tilt. For Z-DNA, reverse signs of Incl and X Dsp. Y Dsp is correct as printed. ROLL and TILT are the simple components of base pair normals along minor and major axes of base pairs. They are the values that were calculated in NEWHEL90 and earlier. VALL, VTIL, VROL, VSLI and VTWI are the total angle betw een base pair normal vectors, and the Tilt, Roll, Slide and Twist calculated relative to a set of local axes halfway between each of the long axes, the short axes, and normal vectors for the two base pairs. They are completely independent of the choice of overall helix axis.