The helix geometry and bending analysis is allowed only for regular double helices of nucleic acids. Z-DNA and all unusual structures which have an 'U' as the first character of the NDB code are excluded. Also structures comprising bulges or looped-out bases are kept out. Nevertheless, there may arise problems for some allowed structures. Some of these cases are listed below. These structures were not excluded because part of the information is valuable. In general, users should always check the plausibility of the results.
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CURVES was not designed for duplexes of this size. CURVES fails if one attempts to calculate groove parameters for these duplexes. In general, bending analysis and calculation of groove width are only allowed for double helices with less than 50 bp. Bending analysis is disabled because none of the geometrical objects implemented in ARC_FIT is adequate for the nucleosome structures. The curvilinear axis looks distorted in the GIF images and the VRML model. A huge number of bonds are displayed between the points of the helical axis which should not be the case. This is a bug, which occurs if the helical axis has more than 99 points. The RASMOL and CHIME models are not affected.
The bending analysis does not yield geometrical parameters for helices with 6 bp, because neither an arc nor a kinked line are fitted. This is a technical limitation of our method. Nevertheless, the axis of 1FJA (and maybe some other helices with 6 bp) is bent as can be seen from the images and 3-dimensional models of the axis.