1. Program "anyhelix" can be used to analyze triplex, quadruplex etc.

   Using fiber31.pdb [i.e., fiber model #31, Poly d(T).Poly d(A).Poly d(T)]
   as an example, here are the procedures on how to analyze it:
   
   [a] fiber31.inp is the input file which gives a listing of each triplet.
       (Please note that the residue numbers can be got by first runing
                   find_pair -pt fiber31.pdb fiber31.bps
        then extract them to fiber31.inp)

   [2] Run "anyhelix" on fiber31.inp, i.e.,
                            anyhelix fiber31.inp
       fiber31.out contains the detailed listing of various parameters.

       For each triplet, the program find all possible base-pairs and
       calculate their base-pair parameters. Anti-parallel bases in a pair,
       such as Watson-Crick base-pair, are noted with "-", e.g. A-T; and
       parallel bases in a pair are noted with "+", e.g., A+T.

   [3] Running "anyhelix" on fiber31.inp also generates several auxiliary
       files with fixed names as follows:
       stacking.pdb -- gives each di-triplet step stacking geometry in a
                      multiple PDB structure data file. For N triplets,
                      there are N - 1 such steps. To extract one from it,
                      you use the utility program "ex_str" as this:
                       ex_str -2 stacking.pdb s2.pdb

                      This will extract the 2nd step (i.e., triplets 2 and
                      3) into a PDB file called "s2.pdb". You can view
                      s2.pdb with RasMol, or generate a high-quality image
                      in PostScript format using program "stack2img" as
                      follows:
                        stack2img -tdco s2.pdb s2.ps

                      Options -t simply adjusts the view of the presentation
                                 by a 90 degrees rotation by z-axis;
                              -d draw H-bonds;
                              -c color by residue;
                              -o filled the base ring
                      These options can be in either lower or upper cases,
                      in any order, and can be combined as illustrated here.
       multiplets.pdb -- similar to stacking.pdb, with each triplet set with
                      reference to its middle frame. Specifically, the view
                      is perpendicular to the mean base plane of the
                      triplet.
       allpairs.pdb -- similar to multiplets.pdb, but for each base-pair

2. "analyze" now also works for a parallel duplex. "para.inp" is an input
   file to "analyze", which corresponds to the parallel Hoogsteen duplex
   formed between chain A (poly d(A)) and chain C (poly d(T)) of
   fiber31.pdb: analyze para.inp

   Of course, "para.inp" is also suitable for "anyhelix": they give
   identical base pair parameters. "analyze" also provide additional
   parameters such as backbone torsion angle, sugar conformation etc.

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xiangjun@rutchem.rutgers.edu (July 9, 2001)
