

1 PLT1D
			[1mPLT1-D[0m 
		    G. J. Quigley,  M. I. T.
			  Sept.  1985

PLT1-D is in  omnigraph  version  of  PLT1,  a molecular graphics 
program, which is provides for the production of color as well as
the normal black and white plots.

2 HISTORY

 The  PLT1  program  was  written  as  an  outgrowth  of  several 
 contouring  and  model  plotting  programs written by the author 
 primarily for  crystallographic  uses.   The  main  functions of 
 this program are  to  allow  arbitrariy  vewing direction of the 
 molecule    provide    for    crystallographic     and/or    non 
 crystallographic symmetery generation.  provide  both stereo and 
 non-stereo  diagrams.   provide  moderately flexible  atom  list 
 selection.  allow for stick and/or space  filling  drawings with 
 provisions for distinguishing atom types.
 
 The PLT1 program was written by Gary J.Quigley  with  advice and 
 discussion  from  a  large  number of coworkers.  In  particular 
 portions  of  the  code  were written by Martha M.Teeter and  by 
 Masayo Watanabi.   Copies of the program and related information 
 may be obtained from
	
 	Dr. Gary J. Quigley
 	Rm 16-743
 	Massachusetts Institute of Technology
 	Cambridge, Massachusetts 02139
 	U.S.A.
 	
 	Phone 617-258-8700, 617-253-4710
 	
2 IMPLIMENTATION
 Requirements and Implimentation
 
 The program was  written  to  run  on a D.E.C.  PDP 11/50 with a 
 floating point processor using  the  RSX11M  version 3 operating 
 system, the FORTRAN IV PLUS  compiller  and  with  32K  words of 
 memory available for the program.   An  attempt was made to keep 
 the code "standard" FORTRAN with the exception  of  those  calls 
 which  associate a given data file with a  logical  unit  number 
 (OPEN, ASSIGN, CLOSE). 
 
 	
 	
2 INTRODUCTION
 In this  section  a  description of a number of the features and 
 procedures used in this program is given.

3 Plotting_System:
 Plotting System: The plotting system is in mm's with
 	+X down the page from top to bottom.
 	+Y across the page from left to right.
 	+Z out of the page toward the viewer.
 	Orientation of Axes: The procedure for determining the position 
	and orientation of the molecule are as follows. 
  1) The origin point is explicitely assigned.
  2) The initial orientation is determined.
  3) A series of succesive rotations are applied.
 
 The molecule is  placed  in  this  system  according to a set of 
 coordinates  in an origin  defining  file  which  has  the  same 
 format as the atoms containing  file and may in fact be the same 
 file.  The origin is defined  by  giving  the number of the atom 
 in this file which will lie at  the  origin.  The orientation is 
 determined by giving the numbers of two atoms  which  will  fall 
 as  near  as possible to being parallel to the  initial  Y-axis.  
 This is followed by giving a list of atoms.   The  least squares 
 plane  through  these  atoms is set perpendicular to the initial 
 Z-axis.
 
 The initial orientation  may  then  be  modified  by a series of 
 successive rotations about the current X, Y or Z axes.
 
 It is worth noting  that views along the normal crystallographic 
 axies may be obtained by  simpley picking the origin as the cell 
 origin (0,0,0) or any desired point  in the cell.  Placing atoms 
 at 0,0,0 and 0,1,0 can define the  Y-axis and an additional atom 
 at 1,0,0 defines the XY plane.
 	
3 Drawing_Limit:
 Drawing Limit:   The  drawing  limits  are determined in several 
 ways.  Thewindow  limits in X and Y in Angstroms are explicitely 
 read in.  The  Z range is somewhat more involved.  A given frame 
 or section (one mono or  a  pair  of  stereo  pictures)  has its 
 thickness determined by the subsection thickness(ZINC)  and  the 
 number  of subsections per section(NSSC).  The  z  thickness  is 
 equally above and below the current z center  value.   If  the z 
 maximum is greater than the current z plus half  the z thickness 
 and  if  the  allowed  number  of  frames has not been  exceeded 
 another  section is created about a new current z center a  half 
 a  z  thickness  above the previous z center.  This procedure is 
 repeated until  either  z  maximum  or  the  maximum  number  of 
 sections is reached.
 	
3 Atom_Selection
 Atoms selection:  The atoms to be included  in  a  given picture 
 may be selected in several ways.  First of  all only those atoms 
 which  fall  within  the  picture  boundries are included in the 
 list of selected atoms.  Only those atoms which are included  in 
 the atoms  selection  list  and  after  undergoing  each  of the 
 symmetery operations are  examined  to determine if they do fall 
 within the frame.
 
 The atoms inclusion list  consists  of  a  list  of  up to eight 
 pairs of numbers.  The  atoms  included  are  those  whose atoms 
 numbers fall within the inclusive range  of  one of the pairs of 
 numbers.  The present version of the  program  accepts a maximum 
 of 2500 atoms.
 
 Up  to  four groups of atoms input may  be  selected.   possible 
 bonds  between  atoms  in the various groups as well  as  hidden 
 surface  elimination  between  atoms of seperate groups will not 
 be carried  out.   Each  group  is completely independent of the 
 other groups.
 	
3 Atom_Symbols:
 ATOM SYMBOLS:   Two types of atoms symbols are provided for both 
 of which are approximately  centered  on  the  atom center.  The 
 first is to use capital  letters,  numerals,  symbols and blanks 
 as provided by the versatec software  character  set.   In  this 
 case  the  desired  letter or symbol is  provided  as  an  ASCII 
 character  in  the  input.  In the second  case  the  "centered" 
 graphics  symbols  are  used  and  the number associated with  a 
 given symbol is provided as input.
 
 In each case the height of the letters in mm's  is  given in the 
 control  cards.   The line thickness of the letters is one  less 
 than  that  specified  for  bonds with the exception of bonds of 
 width one  in  which  the  letters  are also made up of lines of 
 width one.
 
 3 Bonds:
 BONDS:  Bonds are drawn between atoms  in  the  group  which are 
 closer  together than 1) the maximum bond distance  and  2)  the 
 sum of the bond radii for the two types  of  atoms involved plus 
 a   given   bond  incriment.   The  bond  incriment  allows  for 
 variations  from  ideality,  different  bond  types  (double  or 
 single bonds) and  possible error in coordinates.  Crude initial 
 coordinates may produce a  number  of  false bonds while missing 
 others which should be present.   A  few  cycles of idealization 
 with the Konnert and Hendrickson Refinement  program is normally 
 sufficient  to  eliminate  most of these problems  with  minimal 
 atomic  shifts.  (By idealization the author means  the  process 
 of  refining  the  structure  without using the structure factor 
 portion  and  with  moderately  high  damping  on  the  distance 
 shifted).
 
 By setting the maximum bond  distance  to  zero  the  drawing of 
 bonds may be eliminated.  The  bond width is read in explicitely 
 for each atom group as the pen width to be used.

2 CONTROL_CARDS

3 CC-1
       TITLE
 	FORMAT(40A1)
 	TITLE
 	Any desired information. 
 	
3 CC-2 
       Unit Cell Constants
 	FORMAT(6F10.4)
 	A,B,C,ALPHA,BETA,GAMMA
 	A,B,C - unit cell edge lengths in Angstroms.
 	ALPHA,BETA,GAMMA - unit cell angels in degrees.
 	
3 CC-3
       Picture limits
 	FORMAT(7F5.2,I3)
 	XMIN,XMAX,YMIN,YMAX,ZMIN,ZMAX,ZINC,NSEC
 	XMIN,XMAX,YMIN,YMAX - plot limits in Angstroms.
 	ZMIN - center of inital section
 	ZMAX - center of final section
 	ZINC - separation between subsections in Angstroms.
 	       note: ZINC*NSSC (CC 8) is the plot thickness in Angstroms.
 	NSEC - maximum number of sections to be plotted 
	       (two stereo sections count as one section).
 	
3 CC-4	
       Origin and orientation definition file.
 	FORMAT(32A1)
 	ORGFIL
 	ORGFIL- the name of a file containing origin and 
		orientation defining "atoms".
 	
3 CC-5
       Origin, Y-axis and X-axis definitions.
 	FORMAT(5I5)
 	N0,N1,N2,N3,N4
 	N0 - number of the atom at origin..
 	N1,N2 - numbers of two atoms which define the
 		initial Y-axis.
 	N3,N4 - numbers of two atoms which define the
 		initial X-axis.
		note: if N4 is not given then N1 and N3 are used.
		
 	
3 CC-6
       Plane definition
 	FORMAT(16I5)
 	N(I),I=1,16 
 	N(I) - number of atoms to be used to determine least
 		squares plane which is the initial XY plane,
 	note: if N(I) is negative all atoms between N(I-1)
 		and N(I) will be included.
 	
3 CC-7
       Molecular rotation
 	FORMAT(10(I3,F5.1))
 	IAXIS(J),ROT(J),J=1,10
 	IAXIS -  defines the axis about which rotation takes place.
 	IAXIS = 1, X axis
 	      =-1,-X axis
 	      = 2, Y axis
 		etc.
 	ROT(I) - number of degrees of rotation around the I'th axis.
 	
3 CC-8
       Frame, scale and grid parameters
 	FORMAT(F5.1,I3,2F7.4,2F7.1,I3,F7.1,I2,F6.2,I5)
 	SCALE,IGRID,XRSCL,YRSCL,XBOX,YBOX,IFFNFL,FNFLD,ISTR,STRNG,NSSC
 	SCALE - scale of plot in mm/Angstrom
 	IGRID - grid defining parameter
 		IGRID = 0 no grid
 		IGRID = n  a dotted line is drawn every n Angstroms.
 			0.1*n Angstroms between dots.
 		IGRID =-n a + is plotted every n Angstroms.
 	XRSCL - multiplicative constant to correct small distortions in x scale.
 	YRSCL - multiplicative constant to correct small distortions in y scale.
 	XBOX - size of box around plot in x direction given in mm.
 	YBOX - size of box around plot in y direction given in mm.
 	IFFNFL = 0 no action
 	       = 1 draws a line down left edge of length "fnfld"
 	FNFLD - length in mm of fan fold paper being used.
 	ISTR = 0 no stereo
 	     = 1 stereo shift in X
 	     = 2 stereo shift in Y
 	STRNG - stereo angle between views.
 	NSSC - number of subsections per section.
 	
3 CC-9
       Number of symmetry operators.
 	FORMAT(I3)
 	NSYM - number of symmetery operators to be read.
 	
3 CC10
       Atoms file name.
 	FORMAT(64A1)
 	ATMFIL(K)
 	note: if this line is blank CC11-CC15 are not read
 	      and should not be included.
 	
3 CC11
       Atoms parameters
 	FORMAT(F5.1,I3,I3,F5.1,12I5)
 	BNDMAX,BNDWTH,ATMTYP,ATMSIZ,(NI(I),NT(I),I=1,6)
 	BNDMAX - maximum distance beyond which it is assumed 
	         atoms are not bonded.
 	BNDWTH - "pen width" for drawing bonds.
 	ATMTYP = 1 -  letters given in ATMSYB are used for atoms.
 	       = 2 - symbol number given by ATMSYB are used for atoms.
 	ATMSIZ - size of atom symbol in mm.
 	NI(I),NT(I) - initial and final atom numbers of atoms to 
	              be included in the atoms list.
 	
3 CC12
       Atom symbol defination
 	for ATMTYP=1
 	FORMAT(10(3X,A1))
 	ATMSYB(I),I=1,10
 	ATMSYB(I) - character to be used for atom type I,
 		note: capital letters, digits and blanks are 
		      ligitimate characters.
 	for ATMTYP=2
 	FORMAT(10I4)
 	ATMSYB(I),I=1,10
 	ATMSYB(I) - number of centered character to be used 
 		     (see OMNIGRAPH manual).
 	
3 CC13
       Bond defination
 	FORMAT(21F5.2)
 	BNDINC,BNDRAD(I),I=1,20
 	BNDINC - increment to be added to the sum of bond radii 
	         to determine pairs which are to be considered 
		 bonded.
 	BNDRAD(I) - bond radius for atom type I.
 	
3 CC14
       Surface drawing characteristics.
 	FORMAT(I5,10(I5,F4.1),/5X,10(I5,F4.1))
 	ISTYP,(ICRTYP(I),VDWRAD(I),I=1,20)
 	ISTYP - determines type of surface drawing to be drawn.
 	      = 0 -  no surface drawing
 	      = 1 - 
 	      = 2 -  atom boundries to be drawn.
 	      = 3 -  atoms to be "contoured".
 	      = 5 - atoms to be "contoured" and boundries to be drawn.
 	ICRTYP(I) - circle type to be used in "contouring" atom type I.
 	          = 1 -  plane solid circles.
 	          = 2 - dotted circles.
 	          = 3 - dashed circles.
 	          = 4
 	          = 5
 	          = 6 - circles with radial spikes.
 	          = 7 - no circles drawn.
 	          = 8 - dotted circles - dense.
 	          = 9 - dashed circles - dense.
 	VDWRAD(I) radius in Angstroms of surface around atom type I.
 	
3 CC15
       Symmetry inclusion
 	FORMAT(36I2)
 	IFSYM(I),I=1,36
 	IFSYM(I) = 0 if the I'th symmetry operator is not to be used.
 	           1 if the I'th symmetry operator is to be used.
 	
3 CC16-CC21
	same as CC10-CC15.  
 	note:if CC16 is blank CC17-CC21 are not read and 
	     should not be present.
3 CC22-CC27
	same as CC10-CC15.
 	note:if CC22 is blank CC23-CC27 are not read and 
	     should not be present.
3 CC28-CC33
	same as CC10-CC15.
 	note:if CC28 is blank CC29-CC33 are not read and 
	     should not be present.
 	
3 CC34-
       Symmetry cards
 	FORMAT(12F6.3)
 	XX(I),XY(I),XZ(I),YX(I),YY(I),YZ(I),ZX(I),ZY(I),ZZ(I),
	TX(I),TY(I),TZ(I)
 	symmetry related position XS,YS,ZS is related to initial 
	position XO,YO,ZO by
 		(XS)   (XX XY XZ)   (XO)   (TX)
 		(YS) = (YX YY YZ) * (YO) + (TY)
 		(ZS)   (ZX ZY ZZ)   (ZO)   (TZ)
 	
