File: rastep.f

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      PROGRAM RASTEP
********************************************************************************
*
* Usage: 
*    rastep [-h] [-iso] [-Bcolor Bmin Bmax] [-prob xx] [-radius r] [-fancy[0-9]]
*           [-tabulate histogram.file] [-by_atomtype] [-suv_check] [-cn_check]
*
*
*	-auto		auto-orientation of viewpoint
*	-h		suppresses header records in output
*	-iso		forces isotropic B values (spheres rather than
*			ellipsoids) even if ANISOU cards present
*	-aniso		converts isotropic B values into Uij terms so that they
*			can be included in the analysis
*	-Bcolor Bmin Bmax 
*			color by Biso values; Bmin = dark blue, Bmax = light red
*	-Acolor		color by anisotropy;  red < white (A=0.5) < green
*	-prob xx	draws ellipsoids to enclose this 
*			probability level (default = 0.50)
*	-radius		draws bonds with this radius in Angstroms
*			(default = 0.10)
*	-fancy[0-9]	increasingly complex rendition of ellipsoids
*			fancy0  [default] solid surface only
*			fancy1  principle axes + transparent bounding ellipsoid
*			fancy2	equatorial planes only
*			fancy3  equatorial planes + transparent ellipsoid
*			fancy4  longest principle axis only
*			fancy5	for ORTEP lovers - one octant missing
*			fancy6  same as fancy5, with missing octant colored grey
*
*===============================================================================
* The following options are used by parvati scripts
*
*	-tabulate [file]instead of creating a Raster3D input file, 
*			list all atoms with principle axes and anisotropy.
*			Optionally write a histogram of anisotropy to speficied 
*			output file; otherwise output is to stderr 
*
*                       output from -tabulate for this version of rastep
*			ATOM RESNAME RESNUM  EIGEN1 EIGEN2 EIGEN3 ANISOTROPY Uiso
*
*	-com [file]	find <anisotropy> in shells from center of mass
*	-nohydrogens	don't plot hydrogens even if present
*	-mini		small size plot (176x208) with auto-orientation
*	-suv_check	use Suv to validate similarity of bonded ellipsoids
*	-cn_check	use CCuij to check similarity across C-N bonds
*
********************************************************************************
*
* EAM Jul 97	- initial version
* EAM Dec 97	- version 2.4b release
* EAM Jan 98	- add tabulation option
* EAM May 98	- integrate with PARVATI script
* EAM Jun 99	- fix bug (lack of sqrt) in -iso processing, trap read errors
*		  -Acolor flag to color by anisotropy (not yet entirely satisfactory)
* EAM Jul 99	- V2.4l -tab output revised slightly, 
*		  NPD ellipsoids colored magenta
*		  -nohydro flag to suppress drawing hydrogens
*		  -mini    flag to generate smaller pictures
*		  don't draw bonds between atoms with different ALT flags
* EAM Aug 99	- V2.4m 
*		  work harder at suppressing hydrogens
*		  add auto-orientation (NB: scaling is wrong in this case!)
* EAM Dec 99	- V2.5
*		  clean up output formats a little
* EAM Jun 2000	- additional error reporting
* EAM Jul 2000	- apply Bcolor to bonds as well as atoms
* EAM Sep 2000	- Suv similarity test
* EAM Apr 2001	- V2.6 
*		  ORTEP_LIKE ellipsoids (one octant missing)
*		  error count
* EAM Feb 2002	- rework ANISOU and Suv processing to gain back some speed
*		  maybe I should have an array of iso/aniso flags to save
*		  time during testing?
*		  the rest of CARD() array can go too?
*		  all the tests on IF ATOM(I)(1:).eq.'ATOM' are now unneeded
* EAM May 2003	- expand default color table to allow for off-by-one atom names
* EAM Oct 2003	- trap and report 0 values for axial Uij components in input
* EAM May 2006	- initial arrays to 0 for gfortran
* EAM Feb 2008	- 2.7s initialize even more arrays for gfortran
* EAM Aug 2009	- slightly revised output format for -tabulate
* EAM Sep 2009	- Explicitly test CCuij for C-N bonds
* EAM Oct 2009	- report CCuij = if C or N is NPD
*		  -aniso flag
* EAM Mar 2010	- CCuij for phosphate backbone also
* 
*     I/O units for colour/co-ordinate input, specs output, user output
*
      INCLUDE 'VERSION.incl'
*
      INTEGER INPUT, OUTPUT, NOISE
      PARAMETER (INPUT=5, OUTPUT=6, NOISE=0)
      PARAMETER (MAXCOL=5000, MAXATM=300000)
      REAL RGB(3,MAXCOL), VDW(MAXCOL)
      REAL SPAM(5,MAXATM)
      REAL UIJ(6,MAXATM)
      real center(3)
      CHARACTER*24 MASK(MAXCOL),TEST
      CHARACTER*80 ATOM(MAXATM),CARD
      character*3  resname
      character*1  spacer
      LOGICAL MATCH
      logical		hflag, ellipses, bcflag, tflag, atflag, comflag
      logical		acflag, nohydro, mini, auto, aniflag
      integer           fancy
      character*132	flags
c
c     Data structures used for auto-orientation
      real	Rr(3,3), U(4,4), Xmom(5)
c
      COMMON /ASSCOM/ assout, verbose
      integer         assout
      logical         verbose
c
      real	quadric(10), anisou(6)
      real      eigens(4), evecs(4,4), evecinv(4,4), evecit(4,4)
      real      qq(4,4), qp(4,4), temp(4,4)
c
      external	anitoquad
      integer	anitoquad
c
      real	problevel(50)
c
      real start(3),end(3)
      real MARGIN
      parameter (MARGIN = 1.15)
c
      real	Uprin(3), Umean, Usigma, anisotropy, ellipticity
      integer	histogram(20), hislun
      real	anisi(MAXATM), sum_a, sum_a2, anis_mean, anis_sigma
      real	Biso(MAXATM), sum_b, sum_b2, sum_ab
      integer	nanis, niso, nhyd, nonpos
      logical	hwhacky
      integer	nerrors
c
      character*2 atomtype
      integer     natype
c
      real*8	wsum, xsum, ysum, zsum
      real*8	xcom, ycom, zcom
      real	adist(110)
      integer	hdist(110), comlun, dshells
c
c     Support for validation of similarity of bonded atoms
      logical	suvflag, cnflag
      integer	suvlun, suvbad, cnlun, cnbad, ccuijpair
      character*1  prevchain
      character*10 name_i, name_j
      real	anisov(6)
      real      cn_min_ccuij
c
c     Default to CPK colors and VDW radii
      integer DEFCOLS
      parameter (DEFCOLS = 17)
      character*60 defcol(DEFCOLS)
      data defcol /
     & 'COLOUR###### CA ##############   0.175   0.175   0.175  1.70',
     & 'COLOUR###### C  ##############   0.175   0.175   0.175  1.70',
     & 'COLOUR#######C################   0.625   0.625   0.625  1.70',
     & 'COLOUR#######N################   0.125   0.125   1.000  1.60',
     & 'COLOUR#######O################   0.750   0.050   0.050  1.50',
     & 'COLOUR#######S################   1.000   1.000   0.025  1.85',
     & 'COLOUR#######H################   1.000   1.000   1.000  1.20',
     & 'COLOUR#######P################   0.050   0.750   0.050  1.80',
     & 'COLOUR##### CA ###############   0.175   0.175   0.175  1.70',
     & 'COLOUR##### C  ###############   0.175   0.175   0.175  1.70',
     & 'COLOUR######C#################   0.625   0.625   0.625  1.70',
     & 'COLOUR######N#################   0.125   0.125   1.000  1.60',
     & 'COLOUR######O#################   0.750   0.050   0.050  1.50',
     & 'COLOUR######S#################   1.000   1.000   0.025  1.85',
     & 'COLOUR######H#################   1.000   1.000   1.000  1.20',
     & 'COLOUR######P#################   0.050   0.750   0.050  1.80',
     & 'COLOUR########################   1.000   0.000   1.000  2.00'
     &            /
c
c     Critical values for probability ellipsoids of a trivariate normal
c     distribution. From Table 6.1 of ORTEP-III manual (Oak Ridge National
c     Laboratory Report ORNL-6895, 1996). Tabulated below in increments of
c     2% in probability.  Default contours enclose a probability level of
c     50% (critical value 1.5382).
c
	data	problevel /     0.4299, 0.5479, 0.6334, 0.7035, 0.7644, 
     &				0.8192, 0.8694, 0.9162, 0.9605, 1.0026,
     &				1.0430, 1.0821, 1.1200, 1.1570, 1.1932,
     &				1.2288, 1.2638, 1.2985, 1.3330, 1.3672,
     &				1.4013, 1.4354, 1.4695, 1.5037, 1.5382,
     &				1.5729, 1.6080, 1.6436, 1.6797, 1.7164,
     &				1.7540, 1.7924, 1.8318, 1.8724, 1.9144,
     &				1.9580, 2.0034, 2.0510, 2.1012, 2.1544,
     &				2.2114, 2.2730, 2.3404, 2.4153, 2.5003,
     &				2.5997, 2.7216, 2.8829, 3.1365, 6.0000 /
c
c
	assout   = noise
	verbose  = .false.
	hflag    = .false.
	acflag   = .false.
	bcflag   = .false.
	tflag    = .false.
	atflag   = .false.
	comflag  = .false.
	suvflag  = .false.
	cnflag   = .false.
	ellipses = .true.
	hwhacky  = .false.
	nohydro  = .false.
	mini     = .false.
	auto     = .false.
	aniflag  = .false.
	fancy    = 0
	prob     = 0.50
	radius   = 0.10
	nerrors  = 0
c
	prevchain = '@'
c
c	Gfortran is nuts
	wsum = 0
	xsum = 0
	ysum = 0
	zsum = 0
	sum_a = 0
	sum_b = 0
	do i=1,20
	    histogram(i) = 0
	enddo
	do i=1,110
	    adist(i) = 0
	    hdist(i) = 0
	enddo
	do i = 1,3
	    do j = 1,3
	        Rr(i,j) = 0
	    enddo
	enddo
	do i = 1,4
	    eigens(i) = 0
	    do j = 1,4
	        evecs(i,j) = 0
		evecinv(i,j) = 0
		evecit(i,j) = 0
		qq(i,j) = 0
		qp(i,j) = 0
		temp(i,j) = 0
		U(i,j) = 0
	    enddo
	enddo
	do i = 1,5
	    Xmom(i) = 0
	enddo
c
	narg = iargc()
	i = 1
    5	continue
	    call getarg( i, flags )
	    if (flags(1:5) .eq. '-help') goto 701
	    if (flags(1:6) .eq. '-debug') verbose = .true.
	    if (flags(1:2) .eq. '-h') hflag = .true.
	    if (flags(1:4) .eq. '-iso') ellipses = .false.
	    if (flags(1:6) .eq. '-aniso') aniflag = .true. 
	    if (flags(1:4) .eq. '-rad') then
		i = i + 1
		if (i.gt.narg) goto 701
		call getarg( i, flags )
		read (flags,*,err=701) radius
		if (radius.lt.0) radius = 0.0
	    end if
	    if (flags(1:4) .eq. '-pro') then
		i = i + 1
		if (i.gt.narg) goto 701
		call getarg( i, flags )
		read (flags,*,err=701) prob
		if (prob.le.0.) stop 'illegal probability level'
*		If prob > 1 assume they meant it in percent
		if (prob.gt.1.) prob = prob / 100.
	    end if
	    if (flags(1:5) .eq. '-Acol') then
	    	acflag = .true.
		bcflag = .false.
	    end if
	    if (flags(1:5) .eq. '-Bcol') then
		bcflag = .true.
		acflag = .false.
		i = i + 1
		if (i.gt.narg) goto 701
		call getarg( i, flags )
		read (flags,*,err=701) Bmin
		i = i + 1
		if (i.gt.narg) goto 701
		call getarg( i, flags )
		read (flags,*,err=701) Bmax
	    endif
	    if (flags(1:6) .eq. '-fancy') then
		if (flags(7:7).eq.'0') then
		    fancy = 0
		else if (flags(7:7).eq.'1') then
		    fancy = 1
		else if (flags(7:7).eq.'2') then
		    fancy = 2
		else if (flags(7:7).eq.'3') then
		    fancy = 3
		else if (flags(7:7).eq.'4') then
		    fancy = 4
		else if (flags(7:7).eq.'5') then
		    fancy = 5
		else if (flags(7:7).eq.'6') then
		    fancy = 6
		else
		    fancy = 1
		endif
	    endif
	    if (flags(1:4) .eq. '-tab') then
	    	tflag  = .true.
	    	hflag  = .true.
		acflag = .false.
		bcflag = .false.
		fancy  = 0
		do j=1,MAXATM
		    anisi(j) = 0.0
		end do
		hislun = NOISE
		if (i.ge.narg) goto 799
		call getarg(i+1,flags)
		if (flags(1:1) .ne. '-') then
		    hislun = 1
		    open(unit=hislun,file=flags,status='UNKNOWN'
     &              )
		    i = i + 1
		endif
	    endif
	    if (flags(1:4) .eq. '-com') then
		comflag = .true.
		comlun = NOISE
		if (i.ge.narg) goto 799
		call getarg(i+1,flags)
		if (flags(1:1) .ne. '-') then
		    comlun = 2
		    open(unit=comlun,file=flags,status='UNKNOWN'
     &              )
		    i = i + 1
		endif
	    endif
	    if (flags(1:4) .eq. '-suv') then
		suvflag = .true.
		suvlun = NOISE
		suvlimit = 0.975
		if (i.ge.narg) goto 799
		call getarg(i+1,flags)
		if (flags(1:1) .ne. '-') then
		    read (flags,*,err=701) suvlimit
		    i = i + 1
		endif
	    endif
	    if (flags(1:9) .eq. '-cn_check') then
		cnflag = .true.
		cnlun = NOISE
		cn_min_ccuij = 0.95
		if (i.ge.narg) goto 799
		call getarg(i+1,flags)
		if (flags(1:1) .ne. '-') then
		    cnlun = 3 
		    open(unit=cnlun,file=flags,status='UNKNOWN')
		    i = i + 1
		endif
	    endif
	    if (flags(1:8) .eq. '-by_atom') then
		atflag = .true. 
	    endif
	    if (flags(1:8) .eq. '-nohydro') then
		nohydro = .true. 
	    endif
	    if (flags(1:8) .eq. '-mini') then
		mini = .true. 
		auto = .true. 
	    endif
	    if (flags(1:8) .eq. '-auto') then
		auto = .true. 
	    endif
c
	i = i + 1
	if (i.le.narg) goto 5
	goto 799
  701	continue
	write (noise,*) 'Raster3D Thermal Ellipsoid Program ',
     &                  VERSION
  	write (noise,'(/,A)') 'syntax:'
  	write (noise,'(A)')
     &	'rastep	[-h] [-iso] [-Bcolor Bmin Bmax] [-prob Plevel]'
	write (noise,'(A)')
     &  '	[-fancy[0-6]] [-radius R] [-auto]'
	write (noise,'(A,A)')
     &  '	[-nohydrogens] [-suv [suv_limit]] [-cn_check [cnfile]]'
	write (noise,'(A,A)')
     &  '	[-tabulate [tabfile]] [-by_atomtype] [-com [comfile]]'
	call exit(-1)
  799	continue

c
c Critical values for the radius corresponding to a sphere
c enclosing the requested probability level are taken from
c Table 6.1 of the ORTEP manual
	iprob = (prob+0.01)*50.
	pradius = problevel(iprob)

c
	write (noise,800)
	write (noise,*) 'Raster3D Thermal Ellipsoid Program ',
     &                  VERSION
	write (noise,*) 'E A Merritt -  11 Mar 2010'
	write (noise,800)
  800	format('************************************************')
c
	if (.not.ellipses) then
	  write (noise,801) float(iprob)/50.
  801	  format(' Spheres will bound Biso probability level', f5.2)
	else
	  write (noise,802) float(iprob)/50.
  802	  format(' Ellipsoids will bound probability level', f5.2)
	endif
	write (noise,803) pradius
  803	format(' Corresponding critical value           ', f7.4)
	if (aniflag) write (noise,*) 
     &     ' Isotropic atoms will be included in the analysis'
c
      if (acflag) then
      	write (noise,*) 'Atoms will be colored based on Anisotropy'
      endif
c
      if (bcflag) then
	write (noise,*) 'Atom colors will be assigned based on Biso'
	write (noise,*) '    from dark blue = Bmin =', Bmin
	write (noise,*) '      to light red = Bmax =', Bmax
	Umin = Bmin / (8. * 3.14159*3.14159)
	Umax = Bmax / (8. * 3.14159*3.14159)
	Umin = Umin
	Umax = Umax
      endif
c
      if (.not. hflag) then
	WRITE(OUTPUT,'(A,A,I5,A)') 
     &     'Raster3D thermal ellipsoid program ',VERSION,
     &     INT(prob*100.+0.5), '% probability bounds'
     	if (mini) then
	  WRITE(OUTPUT,'(A)') '22  26    tiles in x,y'
	else
	  WRITE(OUTPUT,'(A)') '80  64    tiles in x,y'
	endif
	WRITE(OUTPUT,'(A)') ' 8   8    pixels (x,y) per tile'
	WRITE(OUTPUT,'(A)') '4         3x3 virtual pixels -> 2x2 pixels'
	WRITE(OUTPUT,'(A)') '1 1 1     white background'
	WRITE(OUTPUT,'(A)') 'F         no, shadows are dorky'
	WRITE(OUTPUT,'(A)') '25        Phong power'
	WRITE(OUTPUT,'(A)') '0.15      secondary light contribution'
	WRITE(OUTPUT,'(A)') '0.05      ambient light contribution'
	WRITE(OUTPUT,'(A)') '0.25      specular reflection component'
	WRITE(OUTPUT,'(A)') '0.0       No perspective'
	WRITE(OUTPUT,'(A)') '1 1 1     main light source position'
      end if

c
	if (auto) then
	  ASPECT = 22./26.
	else
	  ASPECT = 80./64.
	endif
c
	NCOL = 0
	NATM = 0
	NANI = 0
	nanis = 0
	niso  = 0
	nhyd  = 0
	nonpos = 0
10    CONTINUE
        READ(INPUT,'(A80)',END=50) CARD
        IF (CARD(1:4).EQ.'COLO') THEN
          NCOL = NCOL + 1
          IF (NCOL.GT.MAXCOL) THEN
            WRITE(NOISE,*) 'Colour table overflow.  Increase ',
     &                     'MAXCOL and recompile.'
            STOP 10
          ENDIF
          READ(CARD,'(6X,A24,3F8.3,F6.2)') MASK(NCOL),
     &          (RGB(I,NCOL),I=1,3), VDW(NCOL)
        ELSEIF (nohydro .AND. CARD(77:78).EQ.' H') THEN
	  goto 10
	ELSEIF (CARD(1:6).EQ.'ANISOU') THEN
	  nani = nani + 1
	  if (card(13:27).ne.atom(natm)(13:27)) goto 14
	  read (card(29:70),*,err=12,end=12) (uij(i,natm),i=1,6)
	  do i=1,6
	  	uij(i,natm) = uij(i,natm) * 0.0001
	  enddo
	  noerr = 1
	  do i=1,3
	  	if (uij(i,natm).eq.0.0) then
		    uij(i,natm) = 0.0001
		    noerr = 0
		endif
	  enddo
	  if (noerr.eq.0) goto 15
        ELSEIF (CARD(1:4).EQ.'ATOM'.OR.CARD(1:4).EQ.'HETA') THEN
          NATM = NATM + 1
          IF (NATM.GT.MAXATM) THEN
            WRITE(NOISE,*) 'Atom array overflow.  Increase ',
     &                     'MAXATM and recompile.'
            STOP 20
          ENDIF
          ATOM(NATM) = CARD
	  uij(1,natm) = -1.0
        ELSEIF (CARD(1:3).EQ.'END') THEN
          GO TO 50
        ENDIF
        GO TO 10
12	write(noise,*) '*** Format problem - ', card(13:70)
	nerrors = nerrors + 1
	goto 10
14	write(noise,*) '*** ANISOU record out of order - ', card(13:70)
	nerrors = nerrors + 1
	goto 10
15	write(noise,*) '*** Illegal ANISOU values - ', card(13:70)
	nerrors = nerrors + 1
	goto 10
*     Come here when EOF or 'END' record is reached
50    CONTINUE
      IF (NATM.EQ.0) THEN
        WRITE(NOISE,*) 'No atoms in input.'
        STOP 30
      ENDIF
*     Load default colors after any that were read in
      IF (NCOL.LE.MAXCOL-DEFCOLS) THEN
        DO i = 1,DEFCOLS
	  NCOL = NCOL + 1
          READ(defcol(i),'(6X,A24,3F8.3,F6.2)') MASK(NCOL),
     &          (RGB(J,NCOL),J=1,3), VDW(NCOL)
        ENDDO
      ENDIF
*
      IF (NCOL.EQ.0) THEN
        WRITE(NOISE,*) 'No colours in input.'
        STOP 40
      ENDIF
      XMAX = -1E20
      XMIN =  1E20
      YMAX = -1E20
      YMIN =  1E20
      ZMAX = -1E20
      ZMIN =  1E20
      DO 100 IATM=1,NATM
        CARD = ATOM(IATM)
c
c	Do a little pre-processing to make later bookkeeping easier
c	At least screen out non-conformant PDB files that contain
c	something obviously not an element type in columns 77:78
c	Hydrogen naming conventions are totally messed up.
c	
     	if (atflag) then
	    resname = card(18:20)
c	    if (resname.eq.'MET' .and. card(14:15).eq.'SD') then
c	    	atom(iatm)(77:78) = 'SD'
c	    end if
	    if ( resname.eq.'HOH' .or. resname.eq.'H2O'
     &	    .or. resname.eq.'WAT') then
     		atom(iatm)(77:78) = 'OW'
	    end if
	    if (atom(iatm)(78:78).ge.'0' .and. atom(iatm)(78:78).le.'9')
     &		atom(iatm)(77:78) = '  '
	end if
	if (nohydro .and. atom(iatm)(77:78).eq.'  ') then
	    do 70 i = 13,16
	    	if (atom(iatm)(i:i).eq.' ') goto 70
	    	if (atom(iatm)(i:i).ge.'1' 
     &		    .and. atom(iatm)(i:i).le.'4') goto 70
		if (atom(iatm)(i:i).ne.'H') goto 71
		atom(iatm)(77:78) = ' H'
   70	    continue
   71	    continue
	end if
	    
c
        TEST = CARD(7:30)
        DO 80 ICOL=1,NCOL
          IF (MATCH(TEST,MASK(ICOL))) THEN
            READ(CARD,'(30X,3F8.3,6X,F6.2)',end=82,err=82) 
     &	        X,Y,Z, Biso(IATM)
	    IF (Biso(IATM).LE.0.0) THEN
	    	nerrors = nerrors + 1
	    	write(noise,*) '*** Illegal Biso ',Biso(IATM),' - ',
     &				atom(iatm)(13:27)
		Biso(IATM) = 0.0
	    ENDIF
            Uiso = Biso(IATM) / (8. * 3.14159*3.14159)
            SPAM(1,IATM) = X
            SPAM(2,IATM) = Y
            SPAM(3,IATM) = Z
	    SPAM(4,IATM) = Uiso
            SPAM(5,IATM) = ICOL
	    RAD  = sqrt(Uiso) * PRADIUS
            XMAX = MAX(XMAX,X+RAD)
            XMIN = MIN(XMIN,X-RAD)
            YMAX = MAX(YMAX,Y+RAD)
            YMIN = MIN(YMIN,Y-RAD)
            ZMAX = MAX(ZMAX,Z+RAD)
            ZMIN = MIN(ZMIN,Z-RAD)
c	    atomtype = CARD(77:78)
c	    if (atomtype.ne.'  ') then
c		weight = amass(atomtype)
c	    else
		weight = 13.4
	    wsum = wsum + weight
	    xsum = xsum + weight * X
	    ysum = ysum + weight * Y
	    zsum = zsum + weight * Z
	    if (uij(1,iatm).lt.0 .and. aniflag) then
		uij(1,iatm) = Uiso
		uij(2,iatm) = Uiso
		uij(3,iatm) = Uiso
		uij(4,iatm) = 0.0
		uij(5,iatm) = 0.0
		uij(6,iatm) = 0.0
c		write(0,*) 'Setting Uiso for atom ',card
	    endif
            GO TO 100
          ENDIF
80      CONTINUE
        WRITE(NOISE,*) 'No colour table mask matches this atom:'
        WRITE(NOISE,*) ATOM(IATM)
        STOP 90
82	continue
	write(noise,*) 'Input format problem in record'
	write(noise,*) CARD
	STOP 90
100   CONTINUE
      XMID = (XMAX+XMIN)/2.
      YMID = (YMAX+YMIN)/2.
      ZMID = (ZMAX+ZMIN)/2.
      TX = -XMID
      TY = -YMID
      TZ = -ZMID
      xcom = xsum / wsum
      ycom = ysum / wsum
      zcom = zsum / wsum
      IF (ASPECT.GE.1.) THEN
*       The X direction is wider than the Y
        XROOM = ASPECT
        YROOM = 1.
        ZROOM = 2.
      ELSE
        XROOM = 1.
        YROOM = ASPECT
        ZROOM = 2.
      ENDIF
      XSPAN = XMAX-XMIN
      YSPAN = YMAX-YMIN
      ZSPAN = ZMAX-ZMIN
      SCALE = MAX(XSPAN/XROOM,YSPAN/YROOM,ZSPAN/ZROOM)
*     Leave a little extra room as a border:
      SCALE = SCALE / 0.90
      if (mini) then
          scale = sqrt(xspan**2+yspan**2+zspan**2) * aspect
          if (scale .lt. 9.) scale = 9.
      end if
*     
*     These are for the center-of-mass table
      DMAX  = MAX( ABS(XMAX-XCOM), ABS(XMIN-XCOM) )**2
     &      + MAX( ABS(YMAX-YCOM), ABS(YMIN-YCOM) )**2
     &      + MAX( ABS(ZMAX-ZCOM), ABS(ZMIN-ZCOM) )**2
      DMAX  = SQRT(DMAX)
      dshells = 100
*
      if (.not. hflag) then
	WRITE(OUTPUT,120) TX,TY,TZ,SCALE
120	FORMAT('1 0 0 0   input co-ordinate + radius transformation'/
     &       '0 1 0 0'/
     &       '0 0 1 0'/
     &       4F10.3)
	WRITE(OUTPUT,'(A)') '3         mixed object types'
	WRITE(OUTPUT,'(A)') '*'
	WRITE(OUTPUT,'(A)') '*'
	WRITE(OUTPUT,'(A)') '*'
      end if
c
c Auto-orientation
c 25-Aug-1999 
c	Find Eigenvectors of moment of inertia tensor.
c	Arrange smallest Eigenvalue along Y, largest along Z.
c Problems:
c	- Could emphasize side-chain over backbone by ignoring 
c	  atoms O and N, but in practice this doesn't seem to help much.
c	- Scaling is wrong, because it was done before rotation.
c
      if (auto) then
      	do 125 iatm = 1, natm
	  if   (atom(iatm)(1:4).ne.'ATOM' 
     &	  .and. atom(iatm)(1:4).ne.'HETA') goto 125
C         if (atom(iatm)(13:15).eq.' O ')  goto 125
C         if (atom(iatm)(13:15).eq.' N ')  goto 125
	  if (atom(iatm)(77:78).eq.' H' .and. nohydro) goto 125
     	  x = spam(1,iatm) - xcom
	  y = spam(2,iatm) - ycom
	  z = spam(3,iatm) - zcom
	  Rq = (x*x + y*y + z*z)
	  Rv = sqrt(Rq)
	  Rr(1,1) = Rr(1,1) + x*x
	  Rr(1,2) = Rr(1,2) + x*y
	  Rr(1,3) = Rr(1,3) + x*z
	  Rr(2,1) = Rr(2,1) + y*x
	  Rr(2,2) = Rr(2,2) + y*y
	  Rr(2,3) = Rr(2,3) + y*z
	  Rr(3,1) = Rr(3,1) + z*x
	  Rr(3,2) = Rr(3,2) + z*y
	  Rr(3,3) = Rr(3,3) + z*z
	  Xmom(1) = Xmom(1) + 1.
	  Xmom(2) = Xmom(2) + Rv
	  Xmom(3) = Xmom(3) + Rq
	  Xmom(4) = Xmom(4) + Rv*Rq
	  Xmom(5) = Xmom(5) + Rq*Rq
  125	continue
  	if (verbose) then
	  write (NOISE,'(/,A,5G13.5)') ' Radial moments:',Xmom
	  write (NOISE,'(A)')        ' Moment of inertia tensor'
	end if
	Rg = sqrt(Xmom(3)/Xmom(1))
	U(1,1) = Xmom(3)
	U(2,2) = Xmom(3)
	U(3,3) = Xmom(3)
	do k = 1,3
	  do l = 1,3
	    U(k,l) = (U(k,l) - Rr(k,l)) / Xmom(1)
	  end do
	  if (verbose) write (NOISE,'(3G13.6)') (U(k,l),l=1,3)
	end do
	call jacobi( U, 3, 4, Eigens, Evecs )
c	Re-order so that long axis is vertical, short axis towards viewer
	  kmax = 1
	  if (Eigens(2).gt.Eigens(kmax)) kmax = 2
	  if (Eigens(3).gt.Eigens(kmax)) kmax = 3
	  kmin = 1
	  if (Eigens(2).le.Eigens(kmin)) kmin = 2
	  if (Eigens(3).le.Eigens(kmin)) kmin = 3
	  kmid = 6 - (kmin + kmax)
	if (verbose) then
	  write (NOISE,'(A,/,3F13.5,10X,3i2)') ' Eigenvalues:', 
     &		Eigens(kmin),Eigens(kmid),Eigens(kmax)
     &		,kmin,kmid,kmax
	  write (NOISE,'(A)') ' Eigenvectors:'
	  do k = 1,3
	    write (NOISE,'(3F13.5)') 
     &		Evecs(k,kmin),Evecs(k,kmid),Evecs(k,kmax)
	  enddo
	end if
     	do k = 1,3
	  U(k,1) = Evecs(k,kmid)
	  U(k,2) = Evecs(k,kmin)
	  U(k,3) = Evecs(k,kmax)
	  U(k,4) = 0.0
	  U(4,k) = 0.0
	enddo
	U(4,4) = 1.0
c	Beware! may be left-handed at this point!
	det = tinv4( evecinv, U )
	if (det .lt. 0.0) then
	  do k = 1,3
	    U(k,3) = -U(k,3)
	  enddo
	endif
c	OK, now it should be right-handed
	WRITE(OUTPUT,'(A)') '# Auto-orientation matrix'
	WRITE(OUTPUT,'(A)') '16'
	WRITE(OUTPUT,'(A)') 'ROTATION'
	do k = 1,3
 	  write (OUTPUT,'(3F13.5)') U(1,k),U(2,k),U(3,k)
	enddo
	WRITE(OUTPUT,'(A)') '# End auto-orientation'
      end if
c
c Label output records
c
      if (.not. tflag) then
	WRITE(OUTPUT,'(A,A)') 
     &	      '# Thermal ellipsoids from Rastep Version ',VERSION
	WRITE(OUTPUT,'(A,F5.2)') '# Probability level',float(iprob)/50.
      end if
c
c Write ellipsoids to input file for render
c
      IF (fancy.eq.0 .and. .not.tflag) GOTO 139
c
c First, optional pass, to write fancy stuff associated with ellipsoids
c
      IATM = 1
  130 CONTINUE
      IF (ATOM(IATM)(1:4).EQ.'ATOM' .OR.
     &    ATOM(IATM)(1:4).EQ.'HETA') THEN
	X = SPAM(1,IATM)
	Y = SPAM(2,IATM)
	Z = SPAM(3,IATM)
	ICOL = SPAM(5,IATM)
	if (bcflag) then
	    call U2RGB( SPAM(4,IATM), Umin, Umax, RED, GREEN, BLUE )
	    RED   = RED*RED
	    GREEN = GREEN*GREEN
	    BLUE  = BLUE*BLUE
	else if (acflag) then
	    call A2RGB( 1.0, RED, GREEN, BLUE )
	    RED   = RED*RED
	    GREEN = GREEN*GREEN
	    BLUE  = BLUE*BLUE
	else 
	    RED   = RGB(1,ICOL)
	    GREEN = RGB(2,ICOL)
	    BLUE  = RGB(3,ICOL)
	endif
	IF (ellipses .and. uij(1,iatm).ge.0.) THEN
	    do i=1,6
		anisou(i) = uij(i,iatm)
	    enddo
	    if (anitoquad(anisou,pradius,quadric,eigens,evecs).lt.0)then
	        write(noise,*) '*** Non-positive definite ellipsoid - ',
     &				atom(iatm)(13:27)
		nonpos = nonpos + 1
	    	nerrors = nerrors + 1
     		Biso(iatm) = 0.0
		goto 138
	    endif
	    goto 132
  132	    continue
	    radlim = pradius * max( eigens(1),eigens(2),eigens(3) )
	    radlim = radlim * MARGIN
c
c	Only for debugging ellipsoids
	    if (verbose) then
	  	write (noise,901) 'ANISOU ',X,Y,Z,ANISOU
	  	write (noise,902) 'QUADRIC',QUADRIC
	  	write (noise,903) 'Eigenvalues', (EIGENS(i),i=1,3),
     &                 'prob', prob,'limiting radius', radlim
     		write (noise,904) 'Evecs ',((evecs(i,j),i=1,3),j=1,3)
	    endif
901	    format(a,3f8.3,6f8.4)
902	    format(a,10f8.3)
903	    format(a,3f8.3,4x,a,f8.3,4x,a,f8.3)
904	    format(a,9f7.3)
c
c	Tabulate principal axes of ellipsoid for each atom
	  if (tflag) then
	    do i=1,3
	    	Uprin(i) = eigens(i)**2
	    enddo
	    if (Uprin(2).gt.Uprin(1)) then
	    	Umean    = Uprin(1)
		Uprin(1) = Uprin(2)
		Uprin(2) = Umean
	    endif
	    if (Uprin(3).gt.Uprin(1)) then
	    	Umean    = Uprin(1)
		Uprin(1) = Uprin(3)
		Uprin(3) = Umean
	    endif
	    if (Uprin(3).gt.Uprin(2)) then
	    	Umean    = Uprin(2)
		Uprin(2) = Uprin(3)
		Uprin(3) = Umean
	    endif
c
c	  Anisotropy we define as Umin / Umax
c	  as in shelxpro output
	    anisotropy  = min(Uprin(1),Uprin(2),Uprin(3))
     &                  / max(Uprin(1),Uprin(2),Uprin(3))
c
c	  But don't count atoms which are perfectly isotropic
	    if (atom(iatm)(77:78).eq.' H') then
	    	nhyd  = nhyd + 1
		if (anisotropy .ne. 1.0) hwhacky = .true.
	    else if (anisotropy .eq. 1.0) then
	    	niso  = niso + 1
	    else
	    	anisi(iatm) = anisotropy
	    	sum_A = sum_A + anisotropy
		sum_B = sum_B + Biso(iatm)
	    	nanis = nanis + 1
	    end if
c
c	  Ellipticity we define as 1 / anisotropy
	    if (anisotropy.eq.0) then
		ellipticity = 0
	    else
		ellipticity = 1. / anisotropy
	    end if
c
c	  Longhi et al (1997) JMB 268, 779-799.
c	  proposed another measure A = sigU / meanU
	    Umean  = (Uprin(1) + Uprin(2) + Uprin(3)) / 3.0
	    Usigma = (Uprin(1)-Umean)**2 
     &		   + (Uprin(2)-Umean)**2 + (Uprin(3)-Umean)**2
	    Usigma = sqrt( Usigma ) / 3.0
	    alonghi = Usigma / Umean
c
c	  Might want to check correlation with Uiso
	    Uiso = SPAM(4,iatm)
c
c	  Cosmetic changes to atom identifier for the sake of sorting
c	  We will force there to be exactly three entities printed.
c	  PDB format is just a mess:
c	  cols 13:16	atom
c	  col     17	alternate conf
c	  cols 18:20	residue
c	  col     22	chain
c	  cols 23:27	resnum
c
	    do i = 16, 13, -1
		if (ATOM(iatm)(i:i) .ne. ' ') j = i
	    enddo
	    do i = 13, 17
		if (ATOM(iatm)(i:i) .ne. ' ') k = i
	    enddo
	    do i = j, k
		if (ATOM(iatm)(i:i) .eq. ' ') ATOM(iatm)(i:i) = '_'
	    enddo
c	    if (ATOM(iatm)(17:17) .ne. ' ') then
c	      do i = 18,19
c		if (ATOM(iatm)(i:i) .eq. ' ') ATOM(iatm)(i:i) = '_'
c	      enddo
c	    endif
	    spacer = ' '
	    if (ATOM(iatm)(22:22) .ne. ' ') then
	      spacer = '_'
	      do i = 23,25
		if (ATOM(iatm)(i:i) .eq. ' ') ATOM(iatm)(i:i) = '_'
	      enddo
	    endif
	    write (output,905) ATOM(iatm)(13:17),
     &            ATOM(iatm)(18:22),spacer,ATOM(iatm)(23:27),
     &            Uprin(1),Uprin(2),Uprin(3),anisotropy,Uiso
905	  format(A5,1X,A5,A1,A5,3F9.4,2X,F9.4,F9.4,F9.4)
c
c	  Also make a histogram of anisotropies
	    i = anisotropy * 20. + 1
	    histogram(i) = histogram(i) + 1
c
c	  And a table of <anis> by distance from center of mass
	    if (comflag .and. anisotropy.lt.1.0) then
	      dist = sqrt( (SPAM(1,iatm)-XCOM)**2 
     &                   + (SPAM(2,iatm)-YCOM)**2 
     &	                 + (SPAM(3,iatm)-ZCOM)**2 )
     	      i = (dist/dmax) * float(dshells) + 1
	      adist(i) = adist(i) + anisotropy
	      hdist(i) = hdist(i) + 1
	    endif
c
c	  End tabulation code
	  endif

c
c	Skip hydrogens if requested
     	  if (nohydro .and. ATOM(IATM)(77:78).eq.' H') goto 138

c
c	Draw principal axes inside bounding ellipsoid
	  if (fancy.eq.1) then
	    do i=1,3
	      size = eigens(i) * pradius - 0.02
	      start(1) = x - size*evecs(1,i)
	      start(2) = y - size*evecs(2,i)
	      start(3) = z - size*evecs(3,i)
	      end(1)   = x + size*evecs(1,i)
	      end(2)   = y + size*evecs(2,i)
	      end(3)   = z + size*evecs(3,i)
	      write (output,907) start, end
907	      format(' 3',/,
     &             3f9.3,' 0.02',3f9.3,' 0.02','  0.5 1.0 0.3')
	    enddo
	  endif
c
c	Draw longest principle axis only
c	(experimental use only - not supported or documented)
	  if (fancy.eq.4) then
	    imax = 1
	    if (eigens(2).gt.eigens(imax)) imax = 2
	    if (eigens(3).gt.eigens(imax)) imax = 3
	    size = eigens(imax) * pradius 
	    imin = 1
	    if (eigens(2).lt.eigens(imin)) imin = 2
	    if (eigens(3).lt.eigens(imin)) imin = 3
	    imed = 6 - (imax+imin)
	    size = size * eigens(imax)/eigens(imed)
	    start(1) = x - size*evecs(1,imax)
	    start(2) = y - size*evecs(2,imax)
	    start(3) = z - size*evecs(3,imax)
	    end(1)   = x + size*evecs(1,imax)
	    end(2)   = y + size*evecs(2,imax)
	    end(3)   = z + size*evecs(3,imax)
	    write (output,907) start, end
	  endif
c
c	Construct 3 quadrics corresponding to the 3 orthogonal planes
c	through the center of our ellipsoid
	if (fancy.eq.2 .or. fancy.eq.3) then
	  eigens(4) = 1.0
	  evecs(4,4)= 1.0
	  det = tinv4( evecinv, evecs )
	  call trnsp4( evecit, evecinv )
	  do k = 1,3
	    do i = 1,4
	    do j = 1,4
		QQ(i,j) = 0.0
	    enddo
	    QQ(i,i) = 1. / (eigens(i)*eigens(i))
	    enddo
	  QQ(k,k) = 1000.
	  QQ(4,4) = -pradius*pradius
	  call tmul4( TEMP, QQ, evecinv )
	  call tmul4( QP, evecit, TEMP )
	  if (acflag) then
	    call A2RGB( anisotropy, red, green, blue )
	    red   = red*red
	    green = green*green
	    blue  = blue*blue
	  endif
	  write (output,151) 14, X,Y,Z, radlim, red, green, blue
	  write (output,152) QP(1,1),QP(2,2),QP(3,3),QP(1,2),QP(2,3),
     &                       QP(1,3),QP(1,4),QP(2,4),QP(3,4),QP(4,4)
	  enddo
	endif
c
      endif
      ENDIF
  138 continue
      IATM = IATM + 1
      IF (IATM.LE.NATM) GOTO 130
c
c     Set transparency for enclosing ellipoids
      if (fancy.eq.1 .or. fancy.eq.3) then
	write (output,'(A,/,A)') '9 Begin transparent ellipsoids','8 '
	write (output,'(A)') ' 15.  0.6   1.0 1.0 1.0   0.6   0 0 0 0'
      else if (fancy.eq.2 .or. fancy.eq.4) then
	goto 160
      endif
c
  139 CONTINUE
c
c If we're just tabulating ellipticity, start making tables
c
      if (tflag) then
	total = 0
	do i = 1,20
	    total = total + histogram(i)
	end do
	if (total.eq.0) then
	    write (noise,*)  'No ANISOU records found'
	    call exit(-1)
	end if
	if (nanis.eq.0) then
	   write (noise,*)   'No anisotropic atoms found'
	   call exit(-1)
	end if
	if (hwhacky) then
	   write(noise,*)
     &	                 'You seem to have anisotropic hydrogens',
     &                   ' - is this some kind of joke?'
     	   nerrors = nerrors + 1
	end if

	write (hislun,'(A)') '# Anisotropy  Fraction   Number'
	write (hislun,'(A)') '#   range     of atoms of atoms'
	do i = 1,20
	    write (hislun,'(2F5.2,3X,F8.3,I10)') 
     &		(float(i)-1.)/20., float(i)/20., 
     &		float(histogram(i))/total, histogram(i)
	end do
c       Calculate mean and sigma of distribution
	sum_a2 = 0.0
	sum_b2 = 0.0
	sum_ab = 0.0
	anis_mean  = sum_A / float(nanis)
	anis_sigma = 0.0
	biso_mean  = sum_B / float(nanis)
	ccoef      = 0.0
	do i = 1,NATM
	    if (anisi(i).ne.0) then
		sum_a2 = sum_a2 + (anisi(i) - anis_mean)**2
		sum_b2 = sum_b2 + (Biso(i)  - biso_mean)**2
		sum_ab = sum_ab 
     &		       + (anisi(i)-anis_mean) * (Biso(i)-biso_mean)
	    end if
	end do
	if (nanis.gt.1) then
	    anis_sigma = sqrt( sum_a2 / float(nanis-1) )
	    ccoef = sum_ab / sqrt(sum_a2 * sum_b2)
	end if

	write (hislun,'(A)')    '#'
	write (hislun,'(A,I10)')'#  number of ANISOU records:',nani
	write (hislun,'(A,I10)')'#       non-isotropic atoms:',nanis
	write (hislun,'(A,I10)')'#           isotropic atoms:',niso
	if (nonpos.gt.0)
     &  write (hislun,'(A,I10)')'# nonpositive-definite APDs:',nonpos
	if (nhyd.gt.0)
     &  write (hislun,'(A,I10)')'#          ANISOU hydrogens:',nhyd
	write (hislun,'(A)') '#'
	write (hislun,'(A,F7.3)')
     &       '# correlation of anisotropy with B_iso:', ccoef
	write (hislun,'(A)') '#'
	write (hislun,'(A)') '#              Anisotropy  B_iso'
	write (hislun,'(A)') '#  AtomType   mean  sigma   mean  number'
	write (hislun,'(A)') '# ---------   ----------- ------  ------'
	write (hislun,'(A,F7.3,F7.3,F7.2,I8)')    
     &       '#|    Total',anis_mean,anis_sigma,biso_mean,nanis

c
c     If we're tabulating ellipticity, but not by atom_type, then we're done
c
	if (.not. atflag) goto 145
  140	continue
c
C     Find an atom type we haven't done yet, exit if none left
c     This only works if the PDB file contains the atom type in
c     columns 77:78 (standard since sometime in 1997, but many
c     files do not conform to this standard)
c
	do i = 1, NATM
	    if (anisi(i).ne.0.0 .and. atom(i)(77:78).ne.'  ') then
	    	atomtype = atom(i)(77:78)
		goto 141
	    end if
	end do
	goto 145
  141	continue

	sum_A     = 0.0
	sum_B     = 0.0
	sum_a2    = 0.0
	biso_mean = 0.0
	natype    = 0
c
c     Loop over atoms looking for the right ones
c
	do i = 1, NATM
	    if (anisi(i).ne.0.0 .and. atomtype.eq.atom(i)(77:78)) then
		natype = natype + 1
		sum_A = sum_A + anisi(i)
	    end if
	end do
	anis_mean  = sum_A / float(natype)
	anis_sigma = 0.0
	do i = 1, NATM
	    if (anisi(i).ne.0.0 .and. atomtype.eq.atom(i)(77:78)) then
		sum_a2 = sum_a2 + (anisi(i)-anis_mean)**2
		biso_mean = biso_mean + Biso(i)
		atom(i)(77:78) = '  '
	    end if
	end do
	if (natype.gt.1) anis_sigma = sqrt( sum_a2 / float(natype-1) )
	biso_mean  = biso_mean / float(natype)

	write (hislun,'(A,4X,A,F7.3,F7.3,F7.2,I8)')    
     &       '#|   ',atomtype,anis_mean,anis_sigma,biso_mean,natype
	goto 140
      end if
      IATM = 1
      goto 150
c
c Write out plot of mean anisotropy as a function of distance from c.o.m.
c The hisclean routine is not strictly necessary; it collapses shells at
c the extreme ranges of distance that contain only a few atoms.
c
  145 continue
      if (comflag) then
      	write (comlun,'(A/A,A/A/A)') '#',
     &	    '# Mean anisotropy as a function of distance',
     &      ' from center of mass',
     &	    '#',
     &	    '#  Distance   <anis>   #atoms'
	call hisclean( adist, hdist, dshells, nanis )
	do i = 1, dshells
	    if (hdist(i).gt.0) then
		adist(i) = adist(i) / float(hdist(i))
		dmid = (dmax/float(dshells))*(float(i)-0.5)
	    	write (comlun,146) dmid, adist(i), hdist(i)
	    endif
	enddo
  146	format(F10.3,F10.3,I10)
      endif
      if (suvflag.or.cnflag) goto 160
      call exit(0)

c
c Second pass write a single sphere or ellipsoid for each atom
c
  150 CONTINUE
      IF (ATOM(IATM)(1:4).EQ.'ATOM' .OR.
     &    ATOM(IATM)(1:4).EQ.'HETA') THEN
     	if (nohydro .and. ATOM(IATM)(77:78).eq.' H') goto 154
	X = SPAM(1,IATM)
	Y = SPAM(2,IATM)
	Z = SPAM(3,IATM)
	ICOL = SPAM(5,IATM)
	if (bcflag) then
	    call U2RGB( SPAM(4,IATM), Umin, Umax, RED, GREEN, BLUE )
	    RED   = RED*RED
	    GREEN = GREEN*GREEN
	    BLUE  = BLUE*BLUE
	else if (acflag) then
	    call A2RGB( 1.0, RED, GREEN, BLUE )
	    RED   = RED*RED
	    GREEN = GREEN*GREEN
	    BLUE  = BLUE*BLUE
	else
	    RED   = RGB(1,ICOL)
	    GREEN = RGB(2,ICOL)
	    BLUE  = RGB(3,ICOL)
	endif
	IF (.not. ellipses) THEN
	    RAD  = sqrt(SPAM(4,IATM)) * PRADIUS
            WRITE(OUTPUT,151) 2, X,Y,Z,RAD,RED,GREEN,BLUE
	ELSE IF (uij(1,iatm).gt.0.) THEN
	    do i=1,6
		anisou(i) = uij(i,iatm)
	    enddo
	    if (anitoquad(anisou,pradius,quadric,eigens,evecs).lt.0)then
	        write(noise,*) '*** Non-positive definite ellipsoid - ',
     &				atom(iatm)(13:26)
     		nerrors = nerrors + 1
     		Biso(iatm) = 0.0
		red   = 1.0
		green = 0.0
		blue  = 1.0
	    endif
	    radlim = pradius * max( eigens(1),eigens(2),eigens(3) )
	    radlim = radlim * MARGIN
	    if (acflag) then
	      anisotropy = min( eigens(1),eigens(2),eigens(3) )
     &	                 / max( eigens(1),eigens(2),eigens(3) )
     	      anisotropy = anisotropy * anisotropy
	      call A2RGB( anisotropy, red, green, blue )
	      red   = red*red
	      green = green*green
	      blue  = blue*blue
	    endif
	    if (fancy.eq.5 .or. fancy.eq.6) then
	      write (output,'(I2,/,A,I2,/,A)') 8,
     &		    ' -1.0 -1.0  -1.0 -1.0 -1.0  0.0  0 0 0',
     &	            fancy-1, 'ORTEP_LIKE'
     	      if (fancy.eq.6) write (output,171) 0.5, 0.5, 0.5
  	      write (output,172) 0, x,y,z, (evecs(i,1),i=1,3)
  	      write (output,172) 0, x,y,z, (evecs(i,2),i=1,3)
  	      write (output,172) 0, x,y,z, (evecs(i,3),i=1,3)
  171	      format('BOUNDING_COLOR ',3F6.3)
  172	      format('BOUNDING_PLANE ',I2,6F10.4)
	    endif
	    write (output,151) 14, x,y,z,radlim,red,green,blue
	    write (output,152) (quadric(i),i=1,10)
	ELSE
	    RAD  = sqrt(SPAM(4,IATM)) * PRADIUS
            WRITE(OUTPUT,151) 2, X,Y,Z,RAD,RED,GREEN,BLUE
  151	FORMAT(I2,/,3(1X,F8.3),4F8.3)
  152	FORMAT(10F12.4)
	ENDIF
      goto 154
      ENDIF
  154 continue
      IATM = IATM + 1
      IF (IATM.LE.NATM) GOTO 150
      IF (fancy.eq.1 .or. fancy.eq.3) then
	write (output,'(A)') '9 end transparent ellipsoids'
      endif
      IF (fancy.eq.5 .or. fancy.eq.6) then
	write (output,'(A)') '9 end ortep ellipsoids'
      endif
  160 continue
c
c Write bonds to file also. Atoms are considered bonded if they lie
c closer to each other than 0.6 * sum of VDW radii.
C If two atoms of different colors are bonded, make half-bond
C cylinders with each color.
C
      if (nerrors.eq.0) write(noise,*) 
     &	 '... no errors found in input file'
      if (radius.eq.0.0 .and. .not.suvflag .and. .not.cnflag) goto 210
      if (suvflag) then
         write (suvlun,'(A,A,F5.3,A)') 
     &      'Checking for neighboring atoms with dissimilar Uij ',
     &	    '(Suv < ',suvlimit,')...'
         suvbad = 0
      endif
      if (cnflag) then
         write (NOISE,'(A,F5.3)') 
     &      'Checking for C-N linkages with CCuij < ', cn_min_ccuij
         cnbad = 0
      endif
c
      DO 202 IATM=1,NATM
     	IF (nohydro .AND. ATOM(IATM)(77:78).EQ.' H') GOTO 202
	if (suvflag .or. cnflag) then
	  if (Biso(IATM).eq.0.0) goto 202
	  if (uij(1,IATM).lt.0.) goto 202
	endif
	XI = SPAM(1,IATM)
	YI = SPAM(2,IATM)
	ZI = SPAM(3,IATM)
	ICOL = SPAM(5,IATM)
	VDWI = VDW(ICOL)
      DO 201 JATM=IATM+1,NATM
	CLOSE2 = 4.537
	DX2 = (XI - SPAM(1,JATM))**2
	if (dx2 .gt. close2) goto 201
	DY2 = (YI - SPAM(2,JATM))**2
	if (dy2 .gt. close2) goto 201
	DZ2 = (ZI - SPAM(3,JATM))**2
	DIST2 = DX2 + DY2 + DZ2
c
c	  Checking for bonded atoms with dissimilar Uij
	  if (suvflag .or. cnflag) then
	    IF (DIST2 .GT. CLOSE2) GOTO 201
	    IF (Biso(JATM).eq.0.0) goto 180
	    if (uij(1,jatm).lt.0.) goto 180
CDEBUG Version 2.6c used explicit test on 0.6*VdW distance
CDEBUG but this is very slow so I have fixed CLOSE2 at the C-S bond length
CDEBUG It might be worth doing a first cut using, say, 2.25A (>S-S bond)
CDEBUG and then only check the actual VdW distance for pairs making the cut
C	    JCOL = SPAM(5,JATM)
C	    VDWJ = VDW(JCOL)
C	    CLOSE2 = (0.6 * (VDWI + VDWJ)) **2
C	    IF (DIST2 .GT. CLOSE2) GOTO 201
CDEBUG Add this section back to see if results match V2.6c numbers
	    similarity = Suv( uij(1,iatm), uij(1,jatm) )
	    if (suvflag .and. (similarity .lt. suvlimit)) then
		write (suvlun,161) 
     &		    ATOM(IATM)(13:17),ATOM(IATM)(18:27),
     &	            ATOM(JATM)(13:17),ATOM(JATM)(18:27),
     &		    similarity
     		suvbad = suvbad + 1
  161	    format(1X,A5,1X,A10,8X,A5,1X,A10,4X,'Suv = ',F8.4)
	    endif
c
c	    Check in particular for C-N links that may be TLS group boundaries
  180	    continue
	    if (cnflag) then
	        ccuijpair = 0
	        if ((ATOM(IATM)(13:15) .eq. ' C ') .and. (ATOM(JATM)(13:15) .eq. ' N ')) then
	            ccuijpair = 1
		endif
	        if ((ATOM(IATM)(13:15) .eq. ' O3') .and. (ATOM(JATM)(13:15) .eq. ' P ')) then
	            ccuijpair = 2
		endif

	        if (ccuijpair.ne.0) then
	            cc = CCuv( uij(1,iatm), uij(1,jatm) )
		    if (ATOM(IATM)(22:22).ne.prevchain) then
	                prevchain = ATOM(IATM)(22:22)
		        write (cnlun,'(1x)')
		        write (cnlun,'(1x)')
		    endif
		    name_i = ATOM(IATM)(18:27)
		    name_j = ATOM(JATM)(18:27)
		    if (name_i(5:5) .eq. ' ') name_i(5:5) = 'X'
		    if (name_j(5:5) .eq. ' ') name_j(5:5) = 'X'
		    do ichar = 6,9
		        if (name_i(ichar:ichar).eq.'_') name_i(ichar:ichar) = ' '
		        if (name_j(ichar:ichar).eq.'_') name_j(ichar:ichar) = ' '
		    enddo
		    write (cnlun,182) name_i, name_j, cc
		    if (cc .lt. cn_min_ccuij) then
		        if (ccuijpair.eq.1) write (NOISE,183) name_i, name_j, cc
		        if (ccuijpair.eq.2) write (NOISE,184) name_i, name_j, cc
		        cnbad = cnbad + 1
		    endif
  182	        format(1X,A10,8X,A10,4X,'CCuij = ',F8.4)
  183	        format(1X,A15,8X,A15,4X,'C-N CCuij = ',F8.4)
  184	        format(1X,A15,8X,A15,4X,'O3''-P CCuij = ',F8.4)
	        endif
	    endif

	    if (tflag) goto 201
	  endif

c	More stringent distance test when drawing bonds
     	  IF (nohydro .AND. ATOM(JATM)(77:78).EQ.' H') GOTO 201
	  JCOL = SPAM(5,JATM)
	  VDWJ = VDW(JCOL)
	  CLOSE2 = (0.6 * (VDWI + VDWJ)) **2
	  IF (DIST2  .GT. CLOSE2) GOTO 201

c	  Don't draw bonds between alternate conformers of same residue
	  IF (ATOM(IATM)(17:17).ne.' '.and.ATOM(JATM)(17:17).ne.' '
     &        .and. ATOM(IATM)(17:17).ne.ATOM(JATM)(17:17)) goto 201
c
c	  Atoms coloured by B value
	  if (bcflag) then
	     write(output,211)
     1		SPAM(1,IATM),SPAM(2,IATM),SPAM(3,IATM),radius,
     2		SPAM(1,JATM),SPAM(2,JATM),SPAM(3,JATM),radius,
     3		1.0, 1.0, 1.0
	     call U2RGB( SPAM(4,IATM), Umin, Umax, RED1, GREEN1, BLUE1 )
	     call U2RGB( SPAM(4,JATM), Umin, Umax, RED2, GREEN2, BLUE2 )
	     write(output,212)
     1		RED1,GREEN1,BLUE1, RED2,GREEN2,BLUE2, 0., 0., 0.
c	  Same color atoms
	  elseif (RGB(1,ICOL) .EQ. RGB(1,JCOL) .AND.
     1       RGB(2,ICOL) .EQ. RGB(2,JCOL) .AND.
     2       RGB(3,ICOL) .EQ. RGB(3,JCOL)) THEN
	    WRITE(OUTPUT,211)
     1         SPAM(1,IATM),SPAM(2,IATM),SPAM(3,IATM),radius,
     2         SPAM(1,JATM),SPAM(2,JATM),SPAM(3,JATM),radius,
     3         RGB(1,ICOL),RGB(2,ICOL),RGB(3,ICOL)
	  ELSE
	    DO K=1,3
		center(K) = (SPAM(K,IATM)+SPAM(K,JATM))/2
	    ENDDO
	    WRITE(OUTPUT,211)
     1         SPAM(1,IATM),SPAM(2,IATM),SPAM(3,IATM),radius,
     2         center(1),center(2),center(3),radius,
     3         RGB(1,ICOL),RGB(2,ICOL),RGB(3,ICOL)
	    WRITE(OUTPUT,211)
     1         center(1),center(2),center(3),radius,
     2         SPAM(1,JATM),SPAM(2,JATM),SPAM(3,JATM),radius,
     3         RGB(1,JCOL),RGB(2,JCOL),RGB(3,JCOL)
	  ENDIF
  201 CONTINUE
  202 CONTINUE
  210 CONTINUE

C211  FORMAT(1H3,/,11(f8.3))
211   FORMAT(1H3,/,3(1x,f8.3),f7.3,3(1x,f8.3),f7.3,3(f6.3))
212   FORMAT(2H17,/,9f8.3)
c
	if (suvflag) then
	    if (suvbad.eq.0) write (suvlun,*) '... No Suv outliers'
	endif
	if (cnflag) then
	    if (cnbad.eq.0) write (suvlun,*) '... No CCuij outliers'
	endif
	if (suvflag .or. cnflag) call exit(0)
c
	write (noise,'(/)')
	write (noise,156) 'X  min max center-of-mass:', XMIN, XMAX, xcom
	write (noise,156) 'Y  min max center-of-mass:', YMIN, YMAX, ycom
	write (noise,156) 'Z  min max center-of-mass:', ZMIN, ZMAX, zcom
	write (noise,156) '     scale:', SCALE
  156	format(1x,a,2f8.2,f10.3)
      END


      LOGICAL FUNCTION MATCH (SUBJ, MASK)
      CHARACTER*24 SUBJ,MASK
      MATCH = .FALSE.
      DO 10 I = 1, 24
        IF (SUBJ(I:I).NE.MASK(I:I) .AND. MASK(I:I).NE.'#') RETURN
10    CONTINUE
      MATCH = .TRUE.
      RETURN
      END

C     Dummy routine to make linker happy (called by QINP in quadric.f)
      SUBROUTINE TRANSF (X,Y,Z)
      RETURN
      END

      SUBROUTINE ASSERT (LOGIC, DAMMIT)
      LOGICAL LOGIC
      CHARACTER*(*) DAMMIT
      COMMON /ASSOUT/ NOISE
      IF (LOGIC) RETURN
      WRITE (NOISE,*) 'ERROR >>>>>> ',DAMMIT
C     STOP 1234
      CALL EXIT(-1)
      END


CCC	Return RGB triple that runs from dark blue at Bmin 
CC	to light red at Bmax
C
	subroutine U2rgb( Uiso, Umin, Umax, r, g, b )
	real              Uiso, Umin, Umax, r, g, b
c
	real    fraction, h, s, v
c
	fraction = (Uiso-Umin) / (Umax-Umin)
	if (fraction.lt.0.) fraction = 0.
	if (fraction.gt.1.) fraction = 1.
	h = 240. * (1.-fraction)
	s = 0.95
 	v = 0.75 + fraction/4.
	call hsv2rgb( h, s, v, r, g, b )
	return
	end


CCC	Return RGB triple that runs from 
CC	red for A=0.0 -> white for A=0.5 -> green for A=1.0
C
	subroutine A2rgb( A, r, g, b )
	real              A, r, g, b
c
	real    fraction, h, s, v
c
	if (A .lt. 0.5) h = 0.0
	if (A .ge. 0.5) h = 120.
	fraction = abs( (A-0.5)*2.0 )
c	s = fraction**2
	s = fraction
	v = 1.0 - s/2.0
	if (A .le. 0.0) then
	    h = 300.
	    v = 1.0
	endif
	call hsv2rgb( h, s, v, r, g, b )
	return
	end


CCC	Color format conversion from Hue/Saturation/Value to Red/Green/Blue
CC	minimal (i.e. NO) error checking
C
	subroutine hsv2rgb( h, s, v, r, g, b )
	real                h, s, v, r, g, b
c
	real    f, p, q, t
	integer i
c
	i = h /60.
	f = h/60. - float(i)
	p = v * (1. - s)
	q = v * (1. - s*f)
	t = v * (1. - s*(1. - f))
	if (i.eq.5) then
	    r = v
	    g = p
	    b = q
	else if (i.eq.4) then
	    r = t
	    g = p
	    b = v
	else if (i.eq.3) then
	    r = p
	    g = q
	    b = v
	else if (i.eq.2) then
	    r = p
	    g = v
	    b = t
	else if (i.eq.1) then
	    r = q
	    g = v
	    b = p
	else
	    r = v
	    g = t
	    b = p
	endif
	return 
	end

CCC	This subroutine is not strictly necessary.
CC	It smooths the histogram/curve of Anisotropy by 
C	distance from center of mass

	subroutine hisclean( value, number, shells, nanis )
c
	integer shells
	real    value(shells)
	integer number(shells)
	integer nanis
c
	integer minshell, maxshell, min10, max10
	integer nsum
	real    vsum
c
	if (nanis .lt. 1200) then
	    shells = shells / 2
	    do i = 1, shells
		number(i) = number(2*i-1) + number(2*i)
		value(i)  = value(2*i-1) + value(2*i)
	    enddo
	endif
c
	do i = shells, 1, -1
	    if (number(i).gt.0) minshell = i
	enddo
	do i = 1, shells
	    if (number(i).gt.0) maxshell = i
	enddo
	nsum = 0
	min10 = minshell
	do i = minshell, shells
	    if (nsum + number(i) .gt. 10) then
		goto 101
	    else
	    	nsum  = nsum + number(i)
		min10 = i
	    endif
	enddo
101	continue
	nsum = 0
	max10 = maxshell
	do i = maxshell, 1, -1
	    if (nsum + number(i) .gt. 10) then
		goto 102
	    else
	    	nsum  = nsum + number(i)
		max10 = i
	    endif
	enddo
102	continue
c
	nsum = 0
	vsum = 0.0
	do i = minshell, min10
	    nsum = nsum + number(i)
	    vsum = vsum + value(i)
	    number(i) = 0
	    value(i)  = 0.0
	enddo
	i = (minshell + min10) / 2
	number(i) = nsum
	value(i)  = vsum
c
	nsum = 0
	vsum = 0.0
	do i = maxshell, max10, -1
	    nsum = nsum + number(i)
	    vsum = vsum + value(i)
	    number(i) = 0
	    value(i)  = 0.0
	enddo
	i = (maxshell + max10) / 2
	number(i) = nsum
	value(i)  = vsum
c
	return
	end