I browsed through the MacDonald et al
. JMB paper quickly, and noticed that the helical parameters were calculated with FREEHELIX (Table 1). The NDB maintains a copy of freehelix98
, if you want to get into the details.
In 3DNA, the helical parameters (including tip/inclination) are calculated for double helices, by default
. However, a similar set of parameters is also available for each strand. For example, the following command: find_pair -s 355d.pdb | analyze
It takes the classic Dickerson B-DNA dodecamer as a "pseudo" continuous single-stranded structure, and outputs (in file "355d.outs") helical parameters for each consecutive dinucleotide. Moreover, the auxiliary files "bp_step.par" and "bp_helical.par" (a bit misnomer with the bp_ prefix) can be used for exact rebuilding, just as for a duplex. See the $X3DNA/doc/tech-details.pdf for how the parameters are calculated. 3DNA uses exactly the same definition for all such parameters, either in a duplex or a single-stranded structure.
DSSR follows the same algorithm as 3DNA (in analyze
) for calculating these parameters. However, the (main) output file contains helical parameters for the duplexes only. DSSR already computes an overwhelming number of parameters, and I've tried to make the default (main) output 'simple'. If you are interested in such single-stranded helical parameter from DSSR, a natural place is a new section in the "dssr-torsions.txt" file. What do you think?