[1] Atomic_?.pdb (? = A, C, G, T or U) 

      Default standard residue geometries used by 3DNA for analyzing and
      rebuilding full atomic nucleic acid structures in PDB format.
		  
      Under subdirectory ATOMIC, there are four sets of standard residue
      geometry files, ADNA_?.pdb, BDNA_?.pdb, NDB96_?.pdb and RNA_?.pdb.
      The base geometries by Clowney et al. (1996) are used and were
      downloaded from the NDB archive. NDB96 set includes just base and C1'
      atoms, without sugar-phosphate backbone. ADNA uses C3'-endo
      sugar-backbone conformation as defined by Arnott's fiber studies, but
      with a chi torsion angle of -160 degrees, average of high resolution
      single crystal X-ray oligonucleotide structures. RNA set is the same
      as ADNA except for an additional O2' atom for each residue. BDNA set
      is similarly defined as ADNA except for the -110 degrees chi torsion
      angle.

      NDB96 set is the default. To use another set, simply copy them to
      overwrite the corresponding Atomic_?.pdb. A utility program,
      "cp_std", can do this automatically for you. You can also choose other
      residue geometries using the utility program "std_base".

[2] Block_BP.alc defines the default base-pair rectangular block. It has
      a size of [10 A (long) -by- 4.5 A (wide) -by- 0.5 A (thick)] and is in
      ALCHEMY format. Is is used for the Calladine-Drew style schematic
      presentation of DNA structures.
    Block_R.alc is for the purine base [4.5 -by- 4.5 -by- 0.5]
    Block_Y.alc is for the pyrimidine base [3.0 -by- 4.5 -by- 0.5]

      Under subdirectory BLOCK, there six block geometry files. Block_M.alc
      has half the size of BLOCK_BP.alc, and can be used if you would like
      the two blocks consisting a base-pair to be of the same size.
      Block_Ms.alc slightly smaller in length than BLOCK_M.alc to avoid
      possible overlaps in a compressed base-pair (i.e. with negative
      stretch). The blocks do not necessarily to be rectangular, as shown in
      Block_R_nr.alc.

[3] Pxyz.dat xyz coordinates of phosphorus atoms with regard to the middle
      dinucleotide reference frame. Four sets were defined, corresponding to
      average values in high resolution A- and B-DNA crystal structures,
      their mean value and TA-DNA. Users can add on new set following the
      format. This file is used by "rebuild" for generating DNA structures
      with only base and phosphorus atoms.

    PxyzH.dat is the same as above except the coordinates are given in the
      middle helical frames.

[4] fig_image.par parameters defining style of the generated XFIG files,
      which can be edited by users to suit their needs.

[5] ps_image.par parameters defining style of the generated PS files, which
      can be edited by users to suit their needs.

[6] baselist.dat: a comprehensive list of currently known base residues and
    their standard counterpart. It makes analysis of unusual DNA and RNA
    structures straightforward

[7] misc_3dna.par: geometric parameters for identifying base-pairs and
    locating helical regions. Mainly used by "find_pair".


[8] my_header.r3d: Sample header file for Raster3D output
    raster3d.par: various parameters for Raster3d output

[9] trans_pep.pdb & trans_pep.alc: trans peptide unit for drawing peptide
    block in protein structures, in the same way as basepair blocks.

[10] Directory RNA_BASES contains the standard bases for calculating the
     authentic "RNA" base-pair parameters (use "cehs" with "-r" option) of
     Babcock and Olson's. Copy these rAtomic_?.pdb files to your current
     directory or directly under BASEPARS to make them known to 3DNA.

[11] col_chain.dat: DNA, protein and ligand color definition. Colors must
     match those in col_mname.dat (164 color names defined by MolScript).
     This file is used my "xmrimg" to generate block + ribbon images.
     --------------------------------------------------------------------------
                 Xiang-Jun Lu <xiangjun@rutchem.rutgers.edu>, July 2002
