ABOUT	SETUP	SEQUENCE	RULES	BOUQUET	OPTIONS	LEGAL
The dynamic and optional specifications may be changed if desired. However, if all you want to do is to generate a single trajectory for a sequence and helicoidal rule you must leave the dynamic and optional items at their preset values. The De Santis et al. rules and the crystallographic averages specify twist, roll and tilt. The Harrington et al. and the Trifonov rules specify only roll and tilt. For the latter, an old rule by Kabsch and Sander is used to specify twist. These combinations have not been sanctioned by the authors of the original rules. None of the rules specify a base rise. A single value is used and the preset value is 3.4Å. You can change this value. You can also override the helicoidal rules and set every base step to a single twist, roll and tilt regardless of the base type. This is actually useful; for example, to generate an absolutely straight sequence and then observe multiple trajectories of this sequence. To generate the trajectory a canonical base pair is translated (base rise) and rotated (twist about the Z-axis, roll about the Y-axis and tilt about the X-axis); each set of operations create a new copy of the original base pair. The rotations can be simultaneous or sequential (the preset method). The remaining two methods are only for testing; the tilt and roll axes are swapped.
Single Trajectory: enter a base sequence, select a helicoidal rule, leave the other settings alone and press the Execute button. Base Sequence Helicoidal Rule Bolshoy De Santis Trifonov Crystal Processing time increases with sequence length and the number of trajectories but it is much less than a minute if yours is the only request. It may take longer to get your results because of network delays. Multiple Trajectories: bouquets are generated only if the size is more than 1 and at least one standard deviation is greater than zero. Bouquet Size trajectories Standard Deviations Å rise | ° twist | ° roll | ° tilt Optional Settings: Leave the following at the preset values unless you really want different settings. Base Rise Å Use Single Helicoidals No, use the selected helicoidal rule Yes, use: ° twist | ° roll | ° tilt Rotation simultaneous sequential sequential: roll and tilt swapped simultaneous: roll and tilt swapped Remove Size Limits: Use of iDNA is free for up to 10000 trajectory-basepairs. To exceed this limit you have to pay US$1 per trajectory-basepair. All major credit cards accepted except Discover.

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