MANIP: an interactive tool for modeling RNA. MANIP allows rapid assembly of separate motifs (each with a specified sequence) into a complex three-dimensional architecture. The already determined modules are present in a database from which they can be extracted with the appropriate sequence. Their assembly is performed in real time with buttons and dials that command rotation and translation of any chosen fragment with respect to the chosen pivot, or that generate all possible variations of any torsion angle within a specified segment either in the 5’ or in the 3’ direction. MANIP automatically recognizes and displays the allowed and nonallowed hydrogen bonds between the residues. The program is interfaced with a rapid and automatic online refinement tool of partial or full assemblies, NUCLIN-NUCLSQ.
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