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RWBROOK: (CCP4: Library)

NAME

rwbrook - Library Subroutines for handling the co-ordinate working format

DESCRIPTION

This document describes the library routines that handle co-ordinate files e.g. reading and writing plus extraction of data to application programs. The current mechanism is that the each identified line is read from the file and the data placed in an intenal buffer. Routines then extract the data from the buffer and pass it to the application program. The current format that is in use is based on the PDB version 2.1 draft format, see separate description.

Authors: John W. Campbell and Adam. C. Ralph

CONTENTS

  1. INTRODUCTION
  2. THE SUBROUTINES
  3. EXAMPLES OF USING THE USING THE LIBRARY ROUTINES
  4. COMMON BLOCKS USED BY THE SUBROUTINES
  5. DESCRIPTION OF INDIVIDUAL SUBROUTINES:

    XYZINIT initialises COMMON blocks must be called first.
    XYZOPEN opens co-ordinate file (by calling XYZOPEN2)
    XYZOPEN2 opens co-ordinate file with option to disable checks for CRYST and SCALE cards
    XYZCLOSE closes co-ordinate fie
    XYZADVANCE reads/writes data from/to file to/from internal buffer.
    XYZATOM extracts various data items from internal buffer e.g. atom name, residue name.
    XYZCOORD extracts x, y, z, occupancy and b from internal buffer
    XYZREWD rewinds file to begining
    XYZBKSP backspaces a line in the file
    PDBREAD reads data items from PDB file.
    RBFROR generates the various orthogonalising matrices
    RBRINV invert 4*4 matrices for conversion between fractional and orthogonal axes
    RBFRAC2 calc transformation matrices bet orthogonal and fractional coordinates
    RBRORF fill or return RF and Ro matrice
    RBFRO1 duplicate of rbfror with a different call
    CVFRAC2 Convert between orthogonal and fractional coordinates and visa-versa
    CVANISOB convert between anisotropic orthogonal Us to crystallographic bs and visa-versa
    RBRCEL Returns Reciprocal cell dimensions, and reciprocal unit cell volume
    RBCELL Returns cell dimensions, and unit cell volume
    WBCELL Writes CRYST1 and SCALEn cards to output file.
    RWNOHEAD Suppress writing of CRYST1 and SCALEn cards to output file by XYZADVANCE or WBCELL
    RES3TO1 Find 3 character residue name from 1 character code and vice versa
    RBRECIP calculates 4SIN**2/L**2
    WREMARK write line to output file
    SFREAD2 matches atomic structure factor with inputted element id.
    RWBFIN copies remaining unread part of file to output.
    RBSPGRP stores a spacegroup name in common.
    WBSPGRP retrieves the spacegroup name from common.
    RBINIT Now obsolete, initialises various COMMON blocks and rewinds file.
    RBROOK Now obsolete, reads ATOM/HETATM card.
    WBROOK Now obsolete, writes ATOM/HETATM card.
    RBFRAC Now obsolete, similar function to RBFRAC2 but with different number of arguments
    CVFRAC Now obsolete, similar function to CVFRAC2 but with different number of arguments
    SFREAD Now obsolete, similar function to SFREAD2 but with different number of arguments

  1. INTRODUCTION

    2. This part describes how to use the RWBROOK libaries to handle co-ordinate data. It will not be a complete account of all the possible instances that may arise but all the routines are described below.

    It may seem a bit strange that simple functions such as CLOSE and REWIND are operated through a specific subroutine. In the future the working format may change however, it is hoped that procedures set out in this part will be independent of the format.

    The old subroutines have been kept to ensure backwards compatiblilty. The compatibility is not absolute however, for instance XYZOPEN or XYZOPEN2 should still be used to open the co-ordinate file. Also, RWBROOK and WBROOK should only be used with orthogonal co-ordinates and not fractional ones.

  2. THE SUBROUTINES

    3. Firstly, the various COMMON blocks must be initialised before reading and writing of files occurs (the COMMON blocks are described below. This is done using XYZINIT, it is called once from the top of the program.

    All co-ordinate files should be opened with XYZOPEN or in special cases XYZOPEN2. The FORTRAN channel number can be assigned automatically. If this is done then it is best that all other files have their channel numbers assigned automatically as well. CCPDPN has been altered to make this easy.

    It is also good practise to close all opened files before the program terminates normally. XYZCLOSE is the subroutine that will close the co-ordinate file.

    The header information from the file is read when the file is opened. This includes the cell, orthogonalisation matrices (and in the future the symmetry). These are then stored in COMMON blocks which then should be extracted by subrotuine calls rather than inclusion of the COMMON blocks in the main program.

    If the cell is present in the file then the matrices for converting between fractional coordinates and orthogonal coordinates in the standard setting will be calculated. If the orthogonalisation matrix is present in the file then the co-ordinates need not be in a standard setting.

    XYZADVANCE has a dual purpose in that it reads/writes data from/to the file into/out of an internal buffer. If the record name is recognised then the data is stored in the buffer. Otherwise the line is ignored but could be echoed to an output file (see the second example). XYZATOM and XYZCOORD then extract the data from the buffer and pass it to the calling program.

  3. EXAMPLE OF USING THE LIBRARY ROUTINES

    4. This example simply reads a PDB file assigned on XYZIN. There is no output file. 
     
C PROGRAM TO READ BROOKHAVEN FILE
C ===============================
C
      REAL X,Y,Z,OCC,BISO,U(6),CELL(6)
      INTEGER IFAIL,ISER,IRS,IXYZIN,IZ,N
      CHARACTER*4 ATNAM,RESNAM,RESNO,SEGID,ID
      CHARACTER*1 CHNNAM,ALTCOD,INSCOD

      EXTERNAL RBCELL,XYZADVANCE,XYZATOM,XYZCLOSE,XYZCOORD,
     +         XYZINIT,XYZOPEN
C
C INITIALISATION CALL
C
      CALL XYZINIT
C
C OPEN FILE
C
      IFAIL = 0
      IXYZIN = 0
      CALL XYZOPEN('XYZIN','INPUT',' ',IXYZIN,IFAIL)
C
C READ COORDINATE RECORDS
C
      N = 0
10    CALL XYZADVANCE(IXYZIN,0,0,*10,*100)
      CALL XYZATOM(IXYZIN,ISER,ATNAM,RESNAM,CHNNAM,IRS,
     +          RESNO,INSCOD,ALTCOD,SEGID,IZ,ID)
      CALL XYZCOORD(IXYZIN,'O','U',X,Y,Z,OCC,BISO,U)
C
C THIS PROGRAM CANNOT HANDLE ANISOTROPIC TEMPERATURE FACTORS
C SO SKIP ANY ANISOU CARDS FOUND
C
      IF (U(2).NE.0.0 .OR. U(3).NE.0.0) THEN
        IF (X.EQ.0.0 .AND. Y.EQ.0.0 .AND. Z.EQ.0.0) GOTO 10
      ENDIF
      N = N + 1
        .
        .
        process data
        .
        .
      GO TO 10
C
C END OF FILE REACHED
C
100   CALL XYZCLOSE(IXYZIN)
      WRITE(6,FMT='(A,I5,A)') ' There are ',N,
     +                        ' atoms in the file'
      CALL RBCELL(CELL,VOL)
      WRITE(6,FMT='(A,3F9.2,3F12.3)') ' The cell is ',CELL
      END

    Here is a further example which reads and writes a file. A set of coordinates are read in and processed. The input file is then re-read and an output file is created with the updated coordinate data. Notice that all the header records plus any REMARK cards will be eched to the output file because of the second call to XYZADVANCE. 

    C PROGRAM TO READ AND UPDATE A BROOKHAVEN COORDINATE FILE
C =======================================================
C
C SPECIFICATION STATEMENTS
C
      REAL XX,YY,ZZ,OCC,BISO
      INTEGER IFAIL,ISER,IRESN,IXYZIN,IXYZOUT,IZ,N,NMAX
      CHARACTER*4 ATNM,RESNM
      CHARACTER*4 ATNAM(1000),RESNAM(1000),RESNO,SEGID,ID
      CHARACTER*1 CHNNAM,ALTCOD,INSCOD
      REAL X(1000),Y(1000),Z(1000),U(6)

      EXTERNAL XYZADVANCE,XYZATOM,XYZCLOSE,XYZCOORD,XYZINIT,
     +         XYZOPEN,XYZREWD
C
C INITIALISE FOR READING AND OPEN FILES
C
      CALL XYZINIT
      IFAIL = 0
      IXYZIN = 0
      IXYZOUT = 0
      CALL XYZOPEN('XYZIN','INPUT',' ',IXYZIN,IFAIL)
      CALL XYZOPEN('XYZOUT','OUTPUT',' ',IXYZOUT,IFAIL)
C
C READ COORDINATES AND STORE THEM
C
      N=0
10    N=N+1
      CALL XYZADVANCE(IXYZIN,0,0,*10,*100)
      CALL XYZCOORD(IXYZIN,'O','U',X(N),Y(N),Z(N),OCC,BISO,U)
C
C SKIP ANISOU CARDS
C
      IF (U(2).NE.0.0 .OR. U(3).NE.0.0) THEN
        IF (X(N).EQ.0.0 .AND. Y(N).EQ.0.0 .AND Z(N).EQ.0.0) THEN
          N = N-1
          GOTO 10
        ENDIF
      ENDIF
      CALL XYZATOM(IXYZIN,ISER,ATNM,RESNM,CHNNAM,
     +         IRESN,RESNO,INSCOD,ALTCOD,SEGID,IZ,ID)
      ATNAM(N) = ATNM
      RESNAM(N) = RESNM
      GO TO 10
C
C REFINE COORDINATES
C
100   NMAX=N-1
      CALL XYZREWD(IXYZIN)
        .
        .
        refine coordinate values
        .
        .
C
C WRITE UPDATED COORDINATE FILE
C
150   CALL XYZADVANCE(IXYZIN,IXYZOUT,0,*200,*200)
      CALL XYZATOM(IXYZIN,ISER,ATNM,RESNM,CHNNAM,IRESN,
     +         RESNO,INSCOD,ALTCOD,SEGID,IZ,ID)
      CALL XYZCOORD(IXYZIN,'O','U',XX,YY,ZZ,OCC,B,U)
C
C IF ANISOU CARD THEN ONLY ATOM NAME ETC. NEED BE CHANGED
C
      IF (U(2).NE.0.0 .OR. U(3).NE.0.0) THEN
        IF (XX.EQ.0.0 .AND. YY.EQ.0.0 .AND. ZZ.EQ.0.0) THEN
          CALL XYZATOM(IXYZOUT,ISER,ATNAM(N),RESNAM(N),
     +      CHNNAM,IRES,RESNO,INSCOD,ALTCOD,SEGID,IZ,ID)
          CALL XYZADVANCE(IXYZOUT,0,0,*200,*200)
          GOTO 150
        ENDIF
      ENDIF
C
C RESET DATA ITEMS AND WRITE TO OUTPUT FILE
C
      CALL XYZATOM(IXYZOUT,ISER,ATNAM(N),RESNAM(N),CHNNAM,
     +      IRES,RESNO,INSCOD,ALTCOD,SEGID,IZ,ID)
      CALL XYZCOORD(IXYZOUT,'O','U',X(N),Y(N),Z(N),OCC,B,U)
      CALL XYZADVANCE(IXYZOUT,0,0,*200,*200)
      GOTO 150

200   CALL XYZCLOSE(IXYZIN)
      CALL XYZCLOSE(IXYZOUT)
      END

  4. COMMON BLOCKS USED BY THE SUBROUTINES

    5. The following common blocks are used to pass information between the subroutines and to hold the contents of the last record read from an input file via XYZADVANCE: 
     
  INTEGER MAXFILESOPEN,FILESOPEN,TYPE,UNIT
  CHARACTER*80 LOGUNIT
  COMMON /RBRKAA/ FILESOPEN,LOGUNIT(MAXFILESOPEN),
                  UNIT(MAXFILESOPEN),TYPE(MAXFILESOPEN)

  MAXFILESOPEN maximum number of files that can be open at any
               one time, = 10.
  FILESOPEN    no. of current coordinate files open.
  LOGUNIT      logical name of file
  UNIT         if the file is PDB then the unit is the physical
               channel opened. If CIF then is related to blocks.
  TYPE         indicates whether PDB (1,-1) or CIF (2,-2). If
               negative then file is output file.



  LOGICAL IFCRYS,IFSCAL,IFEND,MATRIX
  COMMON /RBRKXX/ IFCRYS,IFSCAL,IFEND,ITYP,MATRIX

  IFCRYS       Flag set to .TRUE. if CRYST1 card read, 
               otherwise .FALSE.
  IFSCAL       Flag set to .TRUE. if SCALE cards read, 
               otherwise .FALSE.
  ITYP         Type of last card read.
               =0, No card read.
               =1, 'CRYST1'
               =2, 'SCALE'
               =3, 'TER'
               =4, 'ATOM'
               =5, 'HETATM'
               =6, 'ANISOU'
  MATRIX       Flag set to .TRUE. if orthogonalising 
               and fractionalising matrices set, otherwise 
               .FALSE.
  IFHDOUT      Flag set to .TRUE. if header records written out.
               otherwise .FALSE.


  CHARACTER*1 BROOK,WBROOK,WBROOK1
  COMMON /RBRKYY/ BROOK(80),WBROOK(80),WBROOK1(80)
 
  BROOK        Internal buffer for holding data from input 
               file.
  WBROOK       Internal buffer for holding data for output
               file.
  WBROOK1      Additional buffer for holding data for the 
               output file (specifically for ANISOU card).  


 
  REAL CELL,RR,VOL,CELLAS
  COMMON /RBRKZZ/ CELL(6),RR(3,3,5),VOL,CELLAS(6)

  CELL         Array holding cell dimensions read from 
               CRYST1 card if read (check IFCRYS)
  RR           Array holding some common orthogonalisation
               matrices calculated if CRYST1 cards was read.
               (See description of NCODE in common ORTHOG)
  VOL          Unit cell volume
  CELLAS       Reciprocal cell


 
  INTEGER NCODE,IBRKFL
  REAL RF,RO
  COMMON /ORTHOG/ RO(4,4),RF(4,4),NCODE,IBRKFL
 
  RO           Orthogonalising matrix (only set if CRYST1 or
               SCALE cards read (check the flag MATRIX)
  RF           Fractionalising matrix (only set if CRYST1 or
               SCALE cards read (check the flag MATRIX)
  NCODE        Flag indicating setting found, =0 if not
               recognised.
               =1, a // XO,  c* // ZO (Standard Brookhaven)
               =2, b // XO,  a* // ZO
               =3, c // XO,  b* // ZO
               =4, Hexagonal a + b // XO, c* // ZO
               =5, a* // XO, c // ZO (Rollett)



  REAL AC
  COMMON /RBREC/ AC(6)

  AC           Useful values for calculating d*.



  CHARACTER*11 BRKSPGRP
  COMMON /RBRKSPGRP/BRKSPGRP

  BRKSPGRP     Holds spacegroup name supplied from the s/r
               RBSPGRP.

  5. DESCRIPTION OF INDIVIDUAL ROUTINES:

    6.       SUBROUTINE XYZINIT()
C     =========================
C
C_BEGIN_XYZINIT
C
C	This subroutine initialises the common block RBRKAA ready for reading
C and writing coordinate files. Also, the common blocks associated with 
C storing the header information are initialised. It should be called only 
C once from the top of the program.
C
C Parameters:
C
C       NONE
C
C COMMONS:
C
C         /RBRKAA/ FILESOPEN,LOGUNIT(MAXFILESOPEN),UNIT(MAXFILESOPEN),
C                  TYPE(MAXFILESOPEN)
C
C           FILESOPEN       no. of current coordinate files open.
C           LOGUNIT          logical name of file
C           UNIT            if the file is PDB then the unit is the physical
C                           channel opened. If CIF then is related to blocks.
C           TYPE            indicates whether PDB (1,-1) or CIF (2,-2). If
C                           negative then file is output file.
C
C_END_XYZINIT
C



      SUBROUTINE XYZOPEN(LOGNAM,RWSTAT,FILTYP,IUNIT,IFAIL)
C     ==========================================================
C
C_BEGIN_XYZOPEN
C
C
C      Calls XYZOPEN2 which has an extra paramater for ignoring
C      Symmetry and Cryst cards
C
C Parameters:
C
C         LOGNAM (I)   CHARACTER*(*) but maximum of eight? The logical unit 
C                                    to which the file is assigned
C         RWSTAT (I)   CHARACTER*(*) if 'INPUT' then file is readonly
C                                    if 'OUTPUT' then file is an output file.
C         FILTYP (I)   CHARACTER*(*) if 'CIF' then the file type is treated as
C                                    CIF. If 'PDB' then the file type is 
C                                    treated as PDB. If blank then file type is
C                                    automatically determined for input files 
C                                    and for output file the file type will be
C                                    the same as the first file opened or 
C                                    defaulted to PDB.
C         IUNIT  (I/O) INTEGER       If zero then unit is decided else
C                                    file opened on that unit
C                                    checked against previous data if
C                                    applicable. NOT used with output files.
C         IFAIL  (I/O) INTEGER       On input    = 0 stop on failure 
C                                                = 1 continue on failure
C
C                                    On output   unchanged if OK
C                                                = -1  if error
C
C
C_END_XYZOPEN
C

      SUBROUTINE XYZOPEN2(LOGNAM,RWSTAT,FILTYP,IUNIT,IFAIL,ICRYST)
C     =====================================================
C
C_BEGIN_XYZOPEN2
C
C      Opens a coordinate file for input or output. The channel number can
C be determined automatically or set on input. The header info.
C is also read: cell, orthog. matrix and symmetry.
C This is a version of XYZOPEN with an extra argument to flag whether or
C not the CRYST and SCALE cards are required.
C
C Parameters:
C
C         LOGNAM (I)   CHARACTER*(*) but maximum of eight? The logical unit 
C                                    to which the file is assigned
C         RWSTAT (I)   CHARACTER*(*) if 'INPUT' then file is readonly
C                                    if 'OUTPUT' then file is an output file.
C         FILTYP (I)   CHARACTER*(*) if 'CIF' then the file type is treated as
C                                    CIF. If 'PDB' then the file type is 
C                                    treated as PDB. If blank then file type is
C                                    automatically determined for input files 
C                                    and for output file the file type will be
C                                    the same as the first file opened or 
C                                    defaulted to PDB.
C         IUNIT  (I/O) INTEGER       If zero then unit is decided else
C		  	             file opened on that unit
C                                    checked against previous data if 
C                                    applicable. NOT used with output files.
C         IFAIL  (I/O) INTEGER       On input    = 0 stop on failure 
C                                                = 1 continue on failure
C
C                                    On output   unchanged if OK
C                                                = -1  if error
C
C         ICRYST (I/O) INTEGER       If zero, then check for and use CRYST
C                                    and SCALE cards in input PDB.
C                                    If one, ignore these cards even if
C                                    present.
C
C
C_END_XYZOPEN2


      SUBROUTINE XYZCLOSE(IUNIT)
C     ================================
C
C_BEGIN_XYZCLOSE
C
C	This subroutine closes a coordinate file.
C
C Parameters:
C
C         IUNIT  (I)   INTEGER    Unit number for file
C
C_END_XYZCLOSE
C



      SUBROUTINE XYZADVANCE(IUNIT,IOUT,ITER,*,*)
C     ==================================================
C
C_BEGIN_XYZADVANCE
C
C       This subrouitne reads recognised data lines into a buffer. Optionally,
C if the card is unrecognised (eg REMARK) then the line can be echoed to an
C output file.
C
C Parameters:
C
C       IUNIT  (I) Channel number of the input coordinate file
C
C      These arguments are not relevant for output files.
C        IOUT (I) Logical unit number to which non-atom/hetatm/anisou records
C                 are to be be written (may be blank if reading only)
C        ITER (I) FLAG =1, return if 'ter' card found (via return 1)
C                      =0, do not return when 'ter' card found
C      RETURN 1   Return on TER card if ITER=1
C      RETURN 2   Return on end of file.
C
C_END_XYZADVANCE
C




      SUBROUTINE XYZATOM(IUNIT,ISER,ATNAM,RESNAM,CHNNAM,IRESN,
     *RESNO,INSCOD,ALTCOD,SEGID,IZ,ID)
C     ==============================================================
C
C_BEGIN_XYZATOM
C
C	This subroutine reads or writes the atom name, residue name, 
C chain name etc. into the buffer. XYZADVANCE actually advances a line 
C or atom. The character strings have undefined length in order to make 
C change easier. However, these data items will be strictly defined in 
C the working format.
C
C Parameters:
C
C       IUNIT  (I)  Logical unit of the input coordinate file
C        ISER (I/O) Atom serial number
C       ATNAM (I/O) Atom name        (left justified)
C      RESNAM (I/O) Residue name     
C      CHNNAM (I/O) Chain name       
C       IRESN (I/O) Residue number as an integer
C       RESNO  (O)  Residue number as character, NOT used for output file
C      INSCOD (I/O) The insertion code
C      ALTCOD (I/O) The alternate conformation code.
C       SEGID (I/O) Segid is here to complete PDB standard.
C          IZ  (O)  Atomic number (returned as 7 from ambiguous atoms),
C                   NOT used for output file
C          ID (I/O) Atomic ID related to atomic number (element symbol
C                   right justified), plus the ionic state +2, +3 etc..
C
C_END_XYZATOM
C     




      SUBROUTINE XYZCOORD(IUNIT,XFLAG,BFLAG,X,Y,Z,OCC,BISO,B)
C     =============================================================
C
C_BEGIN_XYZCOORD
C
C	This subroutine reads or writes x, y, z, occupancy and b from/to 
C the internal buffer. The buffer is updated from the file by 
C XYZADVANCE. The coordinates can be input/output (to the subroutine) 
C as orthogonal or fractional. The anisotropic temperature factors can be 
C input/output as orthogonal Us or as crystallographic bs. These are 
C defined below;
C T(aniso) = U(11)*H**2 + U(22)*K**2 + 2*U(12)*H*K + ...
C where H,K,L are orthogonal reciprocal lattice indecies.
C T(aniso) = b(11)*h**2 + b(22)*k**2 + b(33)*k**2 + b(12)*h*k ...    and
C Biso     = 8*PI**2 (U(11) + U(22) + U(33)) / 3.0
C
C Parameters:
C
C       IUNIT  (I)  Channel number of the input coordinate file
C       XFLAG  (I)  For input file
C                     ='F' will get fractional coords. 
C                     ='O' will get orthogonal coords.
C                   For output file
C                     ='F' passed coordinates are fractional
C                     ='O' passed coordinates are orthogonal
C       BFLAG  (I)  For input file
C                     ='B' will get crystallographic bs
C                     ='U' will get orthogonal Us.
C                   For output file
C                     ='B' have crystallographic bs
C                     ='U' have othogonal Us
C           X (I/O) Coordinates (orthogonal angstrom coordinates as
C           Y (I/O)     "        stored)
C           Z (I/O)     "
C         OCC (I/O) Occupancy
C        BISO  (O)  Isotropic temperature factor, NOT used for output file.
C        B(6) (I/O) Anisotropic temperature factor, unless only B(1) defined.
C
C_END_XYZCOORD
C     




      SUBROUTINE XYZREWD(IUNIT)
C     ===============================
C
C_BEGIN_XYZREWD
C
C       This routine is resets pointer to the begining of the file ie.
C rewind the file.
C
C Parameters:
C
C      IUNIT  (I) INTEGER  Channel number for file.
C
C_END_XYZREWD
C




      SUBROUTINE XYZBKSP(IUNIT)
C     ===============================
C
C_BEGIN_XYZBKSP
C
C       This routine is the opposite to XYZADVANCE in that it retreats
C one atom ie. backspacing.
C
C Parameters:
C
C      IUNIT  (I) INTEGER  Channel number for file.
C
C_END_XYZBKSP
C




      SUBROUTINE PDBREAD(ISER,ATNAM,RESNAM,CHNNAM,IRESN,RESNO,
     *X,Y,Z,OCC,B,IZ,SEGID,ID)
C     ========================================================
C
C_BEGIN_PDBREAD
C
C      The subroutine PDBREAD is used to read coordinates from a Brookhaven
C format coordinate file. This routine should not be used stand alone 
C but through XYZADVANCE.
C 
C Parameters
C
C        ISER (O) Atom serial number
C       ATNAM (O) Atom name        (character*4 left justified)
C      RESNAM (O) Residue name     (character*4)
C      CHNNAM (O) Chain name       (character*1)
C       IRESN (O) Residue number as an integer
C       RESNO (O) Residue number   (character*4 or character*5)
C                 If character*5 then the 5th character will be the
C                 insertion code.
C           X (O) Coordinates (orthogonal angstrom coordinates as
C           Y (O)     "        stored)
C           Z (O)     "
C         OCC (O) Occupancy
C        B(6) (O) Temperature factor
C          IZ (O) Atomic number (returned as 7 from ambiguous atoms)
C          ID (O) Atomic ID related to atomic number + ionic state. 
C                 (character*4)
C
C  COMMON BLOCKS
C
C  COMMON /RBRKXX/IFCRYS,IFSCAL,ITYP,MATRIX
C
C      IFCRYS   .TRUE. IF 'CRYST1' CARD READ,  OTHERWISE .FALSE.
C      IFSCAL   .TRUE. IF 'SCALE' CARDS READ, OTHERWISE .FALSE.
C       ITYP    TYPE OF LAST CARD READ =1, 'CRYST1'
C                                      =2, 'SCALE'
C                                      =3, 'TER'
C                                      =4, 'ATOM'
C                                      =5, 'HETATM'
C     MATRIX    .TRUE. IF FRACT/ORTHOG MATRICES CALCULATED
C               .FALSE. IF NOT
C
C  COMMON /RBRKYY/BROOK(80)
C
C      BROOK    CHARACTER*1 ARRAY WHICH IS THE BUFFER FOR PDB FILES
C
C      COMMON/RBRKZZ/CELL(6),RR(3,3,6),VOL,CELLAS(6)
C
C       CELL    CELL DIMENSIONS FROM 'CRYST1' CARD IF READ
C               (CHECK IFCRYS)
C         RR    STANDARD ORTHOGONALISING MATRICES CALCULATED IF THE
C               'CRYST1' CARD WAS READ (CHECK IFCRYS)
C
C  COMMON /ORTHOG/RO(4,4),RF(4,4),NCODE
C
C        RO    ORTHOGONALISING MATRIX (ONLY SET IF 'CRYST1' OR 'SCALE'
C              CARDS PRESENT - CHECK 'MATRIX' FLAG)
C        RF    FRACTIONALISING MATRIX (ONLY SET IF 'CRYST1' OR 'SCALE'
C              CARDS PRESENT - CHECK 'MATRIX' FLAG)
C     NCODE    FLAG INDICATING SETTING FOUND, 0 IF NOT ONE THAT WAS
C              RECOGNISED
C
C_END_PDBREAD
C




      SUBROUTINE RBFRAC2(A,B,C,AL,BE,GA,ARGNCODE)
C     ================================================
C
C_BEGIN_RBFRAC2
C
C
C This subroutine is used to calculate the default transformation
C matrices between orthogonal angstrom and fractional coordinates
C
C
C PARAMETERS
C
C    A,B,C,AL,BE,GA (I) (REAL)     CELL PARAMETERS IN ANGSTROMS AND DEGREES
C    ARGNCODE       (I) (INTEGER)  ORTHOGONALISATION CODE 1-6
C
C_END_RBFRAC2
C




      SUBROUTINE RBRORF(ROO,RFF)
C     =======================
C
C_BEGIN_RBRORF
C
C      SUBROUTINE RBRORF(ROO,RFF)
C
C     Subroutine to  fill or return RF (fractionalising) and Ro
C     (orthogonalising) matrices. 
C
C PARAMETERS
C
C          ROO (I) (REAL(4,4))  4*4 MATRIX TO BE INVERTED
C          RFF (O) (REAL(4,4))  INVERSE MATRIX
C
C common blocks
C
C      COMMON /RBRKXX/IFCRYS,IFSCAL,ITYP,MATRIX
C      COMMON /ORTHOG/RO(4,4),RF(4,4),NCODE
C
C_END_RBRORF




      SUBROUTINE RBRINV(A,AI)
C     =======================
C
C_BEGIN_RBRINV
C
C      SUBROUTINE RBRINV(A,AI)
C
C
C Subroutine to invert 4*4 matrices for conversion between
C fractional and orthogonal axes. 
C
C
C PARAMETERS
C
C           A (I) (REAL(4,4))  4*4 MATRIX TO BE INVERTED
C          AI (O) (REAL(4,4))  INVERSE MATRIX
C
C_END_RBRINV
C




      SUBROUTINE RBFROR
C     =================
C
C_BEGIN_RBFROR
C
C      SUBROUTINE RBFROR
C
C THIS SUBROUTINE CALCULATES MATRICES FOR STANDARD ORTHOGONALISATIONS
c   and cell volume
C
C  this generates the various orthogonalising matrices
C     ' NCODE =1 -  ORTHOG AXES ARE DEFINED TO HAVE'
C                    A PARALLEL TO XO   CSTAR PARALLEL TO ZO'
C     ' NCODE =2 -  ORTHOG AXES ARE DEFINED TO HAVE'
C     '               B PARALLEL TO XO   ASTAR PARALLEL TO ZO'
C     ' NCODE =3 -  ORTHOG AXES ARE DEFINED TO HAVE'
C     '               C PARALLEL TO XO   BSTAR PARALLEL TO ZO'
C     ' NCODE =4 -  ORTHOG AXES ARE DEFINED TO HAVE'
C     '         HEX A+B PARALLEL TO XO   CSTAR PARALLEL TO ZO'
C     ' NCODE =5 -  ORTHOG AXES ARE DEFINED TO HAVE'
C     '           ASTAR PARALLEL TO XO       C PARALLEL TO ZO'
C     ' NCODE =6 -  ORTHOG AXES ARE DEFINED TO HAVE'
C                    A  PARALLEL TO XO   BSTAR PARALLEL TO YO'
C
C   SET UP MATRICES TO ORTHOGONALISE H K L AND X Y Z FOR THIS CELL.
C
C Common Blocks
C
C      COMMON/RBRKZZ/CELL(6),RR(3,3,6),VOL,CELLAS(6)
C      COMMON /RBREC/AC(6)
C
C_END_RBFROR
C




      SUBROUTINE RBFRO1(CEL,VOLL,RRR)
C     ===============================
C
C_BEGIN_RBFRO1
C
C      SUBROUTINE RBFRO1(CEL,VOLL,RRR)
C
C---- This subroutine is a duplicate of rbfror with a different call.
C
C PARAMETERS
C
C   CEL  (I) (REAL(6))     Cell dimensions
C   VOLL (O) (REAL)        Cell volume
C   RRR  (O) (REAL(3,3,6)) Standard orthogonisational matrices
C
C_END_RBFRO1
C




      SUBROUTINE CVFRAC2(X,Y,Z,XX,YY,ZZ,IFLAG)
C     =============================================
C
C_BEGIN_CVFRAC2
C
C      This subroutine is used to convert between the stored  orthogonal  and
C fractional coordinates using the  matrices  set  up  in  the  common  block
C /ORTHOG/ by the subroutine XYZOPEN. If no matrices have been set up then the
C program will stop with an error message.
C                                         
C Call:  CALL CVFRAC2(X,Y,Z,XX,YY,ZZ,IFLAG)
C                                             
C Arguments:
C            
C       X (I)   (REAL)  Input coordinates.
C       Y (I)   (REAL)       "
C       Z (I)   (REAL)       "
C      XX (O)   (REAL)  Output coordinates.
C      YY (O)   (REAL)       "
C      ZZ (O)   (REAL)       "
C   IFLAG (I) (INTEGER)  Flag =0, Convert coordinates from fractional to orthogonal
C                             =1, Convert coordinates from orthogonal to fractional
C
C_END_CVFRAC2
C




      SUBROUTINE CVANISOB(B,IFLAG)
C     =================================
C
C_BEGIN_CVANISOB
C
C      This subroutine is used to convert between crystallographic bs and 
C orthogonal Us. The orthogonal matrices are required, if no matrices have 
C been set up then the program will stop with an error message. The 
C temperature factors are defined below;
C T(anisoU) = U(1,1)*H**2 + U(2,2)*K**2 + U(1,2)*H*K + ... 
C where H,K,L represent the orthogonal representation of the Miller indices
C T(anisob) = b(1,1)*h**2 + b(2,2)*k**2 + b(1,2)*h*k + ...
C thus  U = A * B * AT / (2 * pi**2)  where A is the orthogonalisation matrix
C
C Arguments:
C            
C    B(6) (I/O  (REAL)  Input coordinates.
C   IFLAG (I) (INTEGER)  Flag =0, Convert coordinates from fract. to orthog.
C                             =1, Convert coordinates from orthog. to fract.
C
C_END_CVFRAC
C




      SUBROUTINE RBCELL(CELLD,CVOL)
C     ============================
C
C_BEGIN_RBCELL
C
C      SUBROUTINE RBCELL(CELLD,CVOL)
C
C Returns cell dimensions and unit cell  volume.
C
C PARAMETERS
C     CELLD (O)  (REAL(6))  cell dimensions
C     CVOL (O)  (REAL)     cell volume
C
C Common blocks
C
C      COMMON/RBRKZZ/CELL(6),RR(3,3,6),VOL,CELLAS(6)
C
C_END_RBCELL
C




      SUBROUTINE RBRCEL(RCEL,RVOL)
C     ============================
C
C_BEGIN_RBRCEL
C
C      SUBROUTINE RBRCEL(RCEL,RVOL)
C
C THIS SUBROUTINE RETURNS Reciprocal cell dimensions, and reciprocal
C                       unit cell  volume.
C
C PARAMETERS
C     RCEL (O)  (REAL(6)) reciprocal cell dimensions
C     RVOL (O)  (REAL)    reciprocal cell volume
C
C Common blocks
C
C      COMMON/RBRKZZ/CELL(6),RR(3,3,6),VOL,CELLAS(6)
C
C_END_RBRCEL
C




      SUBROUTINE RES3TO1(RESNM3,RESNM1)
C     ================================
C
C_BEGIN_RES3TO1
C
C      SUBROUTINE RES3TO1(RESNM3,RESNM1)
C
C       FIND 3 CHARACTER RESIDUE NAME FROM 1 CHARACTER CODE OR
C       FIND 1 CHARACTER RESIDUE NAME FROM 3 CHARACTER CODE.
C       SUBROUTINE IS CALLED WITH EITHER RESNM3 OR RESNM1 PREVIOUSLY 
C       ASSIGNED, AND THE OTHER IS ASSIGNED  HERE.
C 
C Parameters
C
C   RESNM3 (I/O)  CHAR*4    3 character residue name
C   RESNM1 (I/O)  CHAR*1    1 character residue name
C
C_END_RES3TO1
C




        SUBROUTINE RBRECIP(IH,IK,IL,S)
C       ==============================
C
C_BEGIN_BRECIP
C
C        SUBROUTINE RBRECIP(IH,IK,IL,S)
C
C---- This subroutine calculates 4SIN**2/L**2
C
C PARAMETERS
C         IH,IK,IL (I) (INTEGER)  reflection indices
C                S (O) (REAL)     4SIN**2/L**2
C
C_END_BRECIP
C




      SUBROUTINE SFREAD2(ID,NG,A,B,C,IWT,IELEC,CU,MO,Ifail)
C     ==========================================================
C
C  Inputs: ID     atom identifier
C          This should match an atom type in the atomsf.lib
C          If an atom is identified as NE2+ say, characters are 
C          subtracted from the ID till a match is found, or there are 
C          no characters left. 
C          EG: Routine tests first NE2+, then NE2, then NE, then N.
C            All matching checks UPPER CASE strings.
C
C          NG     num. of gaussian approximations (2 or 5 (default))
C          IFILFF  .TRUE. if want to open the library file assigned
C                 to ATOMSF (default `atomsf.lib')
C
C  Output: A(4)   coefficient for structure factor calculation
C          B(4)   coefficient for structure factor calculation
C          C      coefficient for structure factor calculation
C          IWT    atomic weight
C          IELEC  number of electrons
C          CU(2)  delta F' and delta F'' for Cu
C          MO(2)  delta F' and delta F'' for Mo
C          Ifail  = -1 if atom not found at all
C                 =  0 OK
C                 =  1 for two gaussian case that does not exist
C




        SUBROUTINE WBCELL(IUNIT,ARGCELL,ARGNCODE)
C       ===============================================
C
C_BEGIN_WBCELL
C
C   This subroutine writes out the cell and orthogonalisation matrices, to 
C the output file. If the input parameters are null then the cell etc. are
C taken from the COMMON blocks.
C
C PARAMETERS
C            IUNIT (I) (INTEGER)   Channel number for output file.
CC       ARGCELL(6) (I) (REAL)      crystallographic cell taken from COMMON
C                                  if cell = 0
C         ARGNCODE (I) (INTEGER)   NCODE number taken from COMMON if NCODE=0
C
C_END_WBCELL
C




        SUBROUTINE WREMARK(IUNIT,LINE)
C       ====================================
C
C_BEGIN_WREMARK
C
C	This subroutine writes a line to the output file. Its main use is for 
C REMARK statements in PDB.
C
C Parameters:
C
C            IUNIT (I) (CHARACTER*(*))  Channel number
C             LINE (I) (CHARACTER*(*))  line to be written, best
C                                       if declared as *80
C
C_END_WREMARK
C



      SUBROUTINE RWBFIN(IUN,IOUT)
C     ===========================
C
C_BEGIN_RWBFIN
C
C       This subroutine copies remaining lines straight from input to
C output.
C
C_END_RWBFIN
C



      SUBROUTINE RBSPGRP(SPGRP)
C     ============================
C
C_BEGIN_RBSPGRP
C
C      SUBROUTINE SUBROUTINE RBSPGRP(SPGRP)
C
C Returns spacegrpup from pdb
C
C PARAMETERS
C     SPGRP (O) (CHARACTER*11) 
C
C Common blocks
C
C      COMMON /RBRKSPGRP/BRKSPGRP
C
C_END_RBSPGRP
C



      SUBROUTINE WBSPGRP(SPGRP)
C     =============================
C
C_BEGIN_WBSPGRP
C
C      SUBROUTINE WBSPGRP(SPGRP)
C
C Sets the internal spacegroup of a pdb file
C
C PARAMETERS
C     SPGRP (I) (CHARACTER*11)
C
C Common Blocks
C
C      COMMON /RBRKSPGRP/BRKSPGRP
C
C_END_WBSPGRP
C
    These routines are now obsolete but are here to maintain backwards compatibility with the version of RWBROOK that was in version 3.2 of CCP4. 
          SUBROUTINE RBINIT(IUNIT)
C     ========================
C
C_BEGIN_RBINIT
C
C      This routine is obsolete and should be removed. Initialises various
C COMMON block variables and rewinds the file.
C
C_END_RBINIT
C




      SUBROUTINE RBROOK(IUNIT,ISER,ATNAM,RESNAM,CHNNAM,IRESN,RESNO,IS,
     *X,Y,Z,OCC,B,IZ,IOUT,MSG1,MSG2,ITER,*,*)
C     ================================================================
C
C_BEGIN_RBROOK
C
C      This subroutine is obsolete and should be removed. May be
C PROBLEM in that routine returns orthogonal coordinates and not fractional
C ones. It presents a combination of XYZADVANCE, XYZATOM and XYZCOORD. The 
C arguments IS, MSG1 and MSG2 are redundant
C
C_END_RBROOK
C




      SUBROUTINE WBROOK(IUNIT,ISER,ATNAM,RESNAM,CHNNAM,IRESN,IS,
     *X,Y,Z,OCC,B,IZ)
C     ================================================================
C
C_BEGIN_RBROOK
C
C      This subroutine is obsolete and should be removed. May be
C PROBLEM in that routine does not cater for IS.
C
C_END_RBROOK
C





      SUBROUTINE RBFRAC(A,B,C,AL,BE,GA,MSG)
C     =====================================
C
C_BEGIN_RBFRAC
C
C       This routine is obsolete and should be removed. The argument
C MSG is redundant.
C
C_END_RBFRAC
C




      SUBROUTINE CVFRAC(X,Y,Z,XX,YY,ZZ,IFLAG,MSG)
C     ===========================================
C
C_BEGIN_CVFRAC
C
C       Another silly obsolete routine that really should be deleted.
C MSG value is in fact useless. Library output controlled by CCPERR.
C
C_END_CVFRAC
C




      SUBROUTINE SFREAD(ID,NG,A,B,C,IWT,IELEC,CU,MO,IFAIL,IFILFF)
C     ===========================================================
C
C_BEGIN_SFREAD
C
C       Obsolete routine should be deleted. IFILFF not used.
C
C_END_SFREAD
C



      SUBROUTINE RWNOHEAD()
C     =====================
C
C_BEGIN_RWNOHEAD
C
C	This subroutine resets the logical variable IFHDOUT in the RWBROOK
C     common block RBRKXX, and should be called once before either
C     XYZADVANCE or WBCELL in order to prevent those routines from writing
C     headers to an output pdb file.
C     Effectively we are fooling the library that the header has already
C     been written.
C
C_END_RWNOHEAD
C