2.34                      ********************
                                  * PDB_CDS WRITE-UP *
                                  ********************


          Interactive program to interchange coordinate files between
        PDB and PHASES formats. The user is first prompted to determine if
        the conversion will be from an input PDB file to a PHASES file. If
        the response is no, the opposite direction is assumed. The user
        is then prompted for input and output file names, and whether
        or not occupancy and/or thermal factors are to be reset. If either
        is to be reset, a prompt for the appropriate new value is given.
        The user is then asked what residue range is to be selected for
        output, and what chain ID (single character). The chain ID must match
        that given in the input file. If no chain ID is present, supply a
        blank in response to the prompt. After writing the selected atoms to
        the output file, the user is then prompted again for another
        range/chain ID. Processing continues until no more ranges/chains
        are requested. If a PHASES style output file is requested, it is
        suitable for use in programs PHASIT or GREF. The program will 
        recognize the 20 standard amino acids with their appropriate three
        letter codes (PDB format, all upper case) or single letter codes
        (PHASES format, upper case). It will also recognize several 
        additional "residue" types, with the following three letter and one
        letter codes, respectively.

        SUL U,  WAT O,  TDP Z,  HEM X,  CAL B,  CAD J,  MAG m,  ZNC z, 

        PO4 p,  ADE a,  CYT c,  GUA g,  THY t,  EXT e

        Note that the codes are case sensitive. If a residue type is input
        that is not one of the above, it still will be processed but will
        be converted to the "extra" type (EXT or e) and a message will be
        output. This presents no problem as residue types are never used
        anywhere in the PHASES package. Howver, if a residue type was
        converted when going to PHASES coordinates, one will have to
        remember to manually convert it back to its original designation
        following each run of PDB_CDS regenerating PDB coordinates.
           When going from PDB to PHASES coordinates, the atom type must
        also be deduced from the atom name. To do this the program will use
        the first one or two characters of the atom name, possibly in
        combination with the residue type. If the atom name starts with the
        letters

        C, N, O, S, P, FE, ZN or MG           (all upper case)

        the appropriate atom type will be recognized. However, if the residue
        type is CAL or CAD, then an atom name starting with CA or CD will
        be recognized as calcium or cadmium, respectively. If the atom name
        is inconsistent with any of the above, it is still processed but the
        type will be set to carbon and a message will be output. Note that even
        if the atom type is not recognized, you can still use the file within
        the PHASES package. You will just have to manually reset the atom type
        code number in the output file to an appropriate number, and possibly 
        input the additional scattering factor information to PHASIT and/or
        GREF. PHASIT and GREF always recognize the code numbers 1,2,...20 as
        corresponding to 
        
        C, N, O, S, Fe+3, Pt+2, Hg+2, Au+3, Pb+2, Os+4, I-, Zn+2, Ca+2, Mg+2,
        Cd+2, U+6, P, Br-, Cl- and Sm+3, respectively. 

        Thus any additional atom types must start with the code number 21.
        See the PHASIT and GREF writeups for details on how to input the
        scattering factors.

        The residue names are never used within the PHASES package.


                              ***** FILES *****

        INPUT - either a standard PDB file or a PHASES style coordinate
                file

        OUTPUT - the inverse of what was input.