[1] Four set of PDB files are given here to illustrate the analysis procedures:
    adh026  --- A-DNA
    bdl084  --- B-DNA
    pd0001  --- nucleosome DNA structure
    pde0128 --- DNA-protein complex with A-DNA and B-DNA junction

    The *.inp files for each of the DNA structure were generated with
    "find_pair". Using bdl084.pdb as an example:
                       find_pair -t bdl084.pdb bdl084.inp

    The "-t" option will also take HETATM records in PDB file into
    consideration. While it does matter for bdl084.pdb here, it is necessary for
    structures involving non-standard A, T, C, G and U residues which are
    sometimes put into HETATM records (e.g., in RNA). As a rule, always put "-t"
    option to "find_pair".

    With "bdl084.inp" in hand, run "analyze" against it to get various
    structural parameters:
                               analyze bdl084.inp

    The above to step can be combined:
                    find_pair -t bdl084.pdb stdout | analyze

    The four structures can be analyzed simultaneously as follows:
              analyze adh026.inp bdl084.inp pd0001.inp pde0128.inp

    In addition to the main parameter output file (*.out), each run of "analyze"
    also generates a serial of other files with fixed names. Each time "analyze"
    is executed, these files are re-written unless renamed.

    Finally "multi_str.inp" contains all the above *.inp files in one, and is
    suitable for "manalyze" which is a Perl script calling "analyze":
                           manalyze multi_str.inp
 
[2] Rebuilding with the sugar-phosphate backbone
    The rebuilding of a DNA structure rely on its base sequence and associated
    base-pair and step parameters, and a set of standard Atomic_?.pdb data file.
    
    The rebuilding algorithm is rigorous as far as the base-pair geometry is
    concerned. However, approximate sugar-phosphate conformations can be
    attached to the bases as they are built. This way, you get a full atomic
    structure with the sugar-phosphate backbone.

    In directory BASEPARS/ATOMIC/, there are four set of standard PDB files,
    corresponding to A-DNA (C3'-endo), B-DNA (C2'-endo), RNA (C3'-endo plus
    O2') and NDB96 (default, no backbone). The base geometry in each set are
    identical.

    To use a set other than the default, simply copy these files to their
    Atomic_?.pdb counterpart. I.e., BDNA_stdA.pdb ---> Atomic_A.pdb
    A simple Perl script "cp_std" helps with this process. 
    For example:
                       cp_std BDNA
    will put the B-DNA set into your current directory (as in this directory).
    Please note that 3DNA search for Atomic_?.pdb files in the order of
     a). current directory;
     b). $X3DNA/BASEPARS (default);
     c). $HOME/BASEPARS (if $X3DNA is not defined)

   To rebuild bdl084 with standard C2'-endo B-DNA sugar-phosphate backbone,
   here is the procedure:
                    find_pair -t bdl084.pdb stdout | analyze
   You get "bp_step.par" which contains base-pair sequence and step parameters.
   (Another file, "bp_helical.par", which contains helical parameters, is also
   suitable for the following rebuilding process.)
                      rebuild -atomic bp_step.par temp.pdb
   Use RASMOL to have a look of "temp.pdb". It contains explicitly all valence
   bonds.

   To verify that the algorithms used in 3DNA is rigorous and reversible,
   re-analyze the rebuilt structure "temp.pdb", and you will get the same
   base-pair parameters as directly from "bdl084.pdb". Alternatively, you
   could superimpose "temp.pdb" to "bdl084.pdb", and you will find that the
   RMSD is virtually zero if only base atoms (i.e., excluding backbone) are
   considered. If the sugar-phosphate backbone atoms (full-atom) are also
   used, the results for three DNA structures are as follows:
 
                                     pd0001   bdl084   adh026
                      full-atom       0.82     0.73     0.52*
                      base-atom       0.05     0.02     0.03

    (In rebuilding full-atomic model, regular sugar-phosphate backbone
    conformation was used: B-type for pd0001 and bdl084, and A-type for
    adh026. It should be noted that the labeling of O1P/O2P atoms in adh026
    from the NDB is not consistent with the convention. Thus the RMS values
    for full-atom corresponds the those after correction with a utility
    program "o1p_o2p".)

    By matching Atomic_?.pdb with base sequence, it is also possible to
    generate a DNA structure with mixed A- and B-DNA conformation, as in
    pde0128.pdb.

                                  ==============================================
                                     Xiang-Jun Lu (xiangjun@rutchem.rutgers.edu)
                                                                    July 6, 2001
