ABOUT	SETUP	SEQUENCE	RULES	BOUQUET	OPTIONS	LEGAL
If there is no problem with your input data you will get a result page containing a link to download a kinemage file. This contains the trajectory or trajectories. If you are properly set up, clicking on the kinemage link will cause the trajectory to be downloaded to your hard disk and it will be handed over to your MAGE application for display. You must pick up the kinemage file immediately; it will remain on the server for only a short while. If you have not already done so you need to download the MAGE application and set your browser to use it as a helper application. You can download MAGE from the official kinemage site. There should be no need to set preferences manually. Just click on a kinemage link. If you are not set up to handle kinemage files yet, your browser should ask how you want to deal with the file. Elect to pick an application. Once you have located your MAGE application, the file will be downloaded and MAGE will be called to handle the kinemage file. Your browser should then remember this setting for all future kinemage links. If you have to make a manual setting, here are the information you need: Description Kinemage MIME Type chemical/x-kinemage Suffix kin Press the button to pick an application and locate your copy of MAGE. If you are using one of the Macromolecular Modeling Computers you do not need to download and install the application but you need to set the application path to: Application /gt/bin1/mage %s
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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