ABOUT	SETUP	SEQUENCE	RULES	BOUQUET	OPTIONS	LEGAL
The specified sequence and helicoidal prediction rule is used to generate a set of mean helicoidals. In the standard mode these helicoidals are used to generate a single trajectory. If you specify at least one non-zero standard deviation and if you specify more than one trajectory, then a bouquet of trajectories will be created. Samples are drawn for the specified means and standard deviations to generate the trajectories. The product of the number of base pairs and the number of trajectories must not exceed 10000. Thus, you can ask for 100 samples of a 100 base pair sequence or 1000 samples of a 10 base pair sequence and so on. Bear in mind that processing time increases with the sequence length and the number of trajectories. At the limits in the sequence length and bouquet size, processing time is just under six seconds and the kinemage file is over 400 KB. You should bear these in mind as you pick a bouquet size, especially if you have a slow network connection.
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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