This example uses a DNA double helix of 12 base pairs and two structures of the same sequence but different conformations.
cp /srv/local/dandw/examples/dna/comparison/* .
source curves.com
axis.out
which should look like this:
Base Pair: C 1- G 24
Axis-Base Pair Parameters
Config # XDP YDP INC TIP
1 -0.61 0.18 5.31 0.73
2 -5.29 0.00 19.46 0.00
3 0.00 0.00 1.46 0.00
... etc
where XDP = x displacement, YDP = y displacement, INC = inclination, and TIP = tip as defined.
backbone.out
which should look like this:
Base: C 1
Conformational Angles L.H.S
Config # d e z a b g c f
1 156.59 218.62 216.44 294.34 169.89 40.26 254.80 161.67 56.56
2 83.21 174.59 314.64 270.52 210.98 47.22 206.84 13.73 38.74
3 139.47 226.82 203.13 319.25 135.58 37.42 258.11 154.69 39.73
... etc
where d, e, z, a, b, g, c, and f refer to delta, epsilon, zeta, alpha, beta, gamma, chi, and phi angles.
base .out
Base Pair: C 1- G 24
Intra-Base Pair Parameters
Config # SHR STR STG BKL PRP OPN
1 -0.98 -0.19 -0.14 3.68 -16.29 -4.94
2 0.00 -0.11 0.15 0.02 11.42 -0.81
3 0.00 0.00 -0.08 0.01 -13.27 0.01
.. etc
where SHR = shear, STR = stretch, STG = stagger, BKL = buckle, PRP = propeller, and OPN= open as defined.
and you have six postscript output files as below. Notice the multiple lines in these dials and windows. The first value is drawn as a solid line and every subsequent value is shown using dashed lines with number of dashes proportional to the index of the analyzed structure.
If you give the command:
source plate.com
you will have Postscript files called page1.ps that look like this:
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