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iDNA is an experimental program. We have concentrated on the web interface for this iteration of the program. No attention has been paid to the scientific and computational aspects of the program except to the extent of getting reasonable results. For now, iDNA is available only for testing and development. iDNA must not be used for research. TO DO: 1. For sequences shorter than 31 base pairs, generate base pairs in their all-atom glory, not connected to the backbones rendered as ribbons, arrow heads on the 3' ends. Need coordinates of AT, TA, CG, GC pairs properly positioned on the origin and oriented to the coordinate axes. 2. Correct angle signs in the helicoidal rules, are they consistent with the sign convention used in the rotation matrix? 3. Proper citations for the helicoidal rules. Source of the crystal averages. 4. Expand the single helicoidal option to allow entry of user rules, 16 entries instead of one per helicoidal parameter. It would make it more tedious to specify single helicoidals though. 5. Proper typical values of the SDs, current values are plucked from the ether. Alternatives to entry of SDs: persistence length for roll and tilt (and anisotropy for distribution into roll and tilt modes) and longitudinal and torsional moduli for rise and twist. 6. Need a proper legal statement, UAB legal? Need a way for users to cite iDNA in works that make use of it. 7. Currently rules are hardwired in associative arrays, put them in ndbm files, a pair per rule. It will make it much easier to implement additional rules. Need separate utility to create the files. |
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