
1 FOURIER

2 Introduction
 
 Package consists of four  consecutive  programs  FORIN,  EXPAND, 
 FFT  and  PEAKS.  FORIN  reads  a  standard  set  of  input  and 
 generates  the  controle  card  files for  the  remaining  three 
 programs.   EXPAND  expands  an  asymmetric  set   of  structure 
 factores  into  a  triclinic set of Beevers-Lipson coefficients.  
 The  EXPAND  input  consists of the controle cards generated  by 
 FORIN,  a  set  of  equivalent  position cards and the structure 
 factors in the form for PROLSQ. 

 The  names of the latter two files are contained in the controle 
 card file.   FFT transforms the output of EXPAND into an integer 
 map (INTEGER*2) written  one row per record.  FFT reads a set of 
 controle cards written by  FORIN,  the  EXPAND  output  file and 
 produces a map file the  name  of  which is in the controle card 
 file.  PEAKS reads in the  electron density map and searches for 
 positive  and negative peaks.  The input  consists  of  controle 
 cards produced by FORIN and the map from  FFT.   The output is a 
 list  of  peaks  including  interpolated  peak  position  and an 
 estimate  of  number of electrons and if desired an output  file 
 contianing  peaks  as  water  molecules  in the form for PROLSQ, 
 STRCON, PLT1 etc. 

2 Credits
 
		 This package was assembled by 
			Gary J. Quigley 
	   M.I.T. Laboratory of Molecular Structure. 
		       M.I.T. Rm 16-743,
		    Cambridge, Mass., 02139 
			   telephone 
		 617-258-8700 or 617-253-4710. 
 
	Programs contributed by
	FORIN   - G.J.Q.
	EXPAND  - Richard Fischer University of Oregon, Eugene Oregon
	        - with corrections and modifications by G.J.Q.
	FFT     - Richard Fischer and Ward Smith U.C.L.A.
	        - modifications by G.J.Q.
	PEAKS   - G.J.Q.

2 Forin_Input

3 Example
   Sample input cards - FORIN.DAT for d(CpGpTpApCpG)+ daunomycin.
 ================================================================
  D-CGTACG+Dau 
  27.92,27.92,52.89,90.0,90.0,90.0,0.0
 SFSNW.BIN
  92, 3, 0.0, 0.25, 1.00, 0.0, 0.0,
 BCA
  0,63,64, 0,63,64, 0,127,128,
 SG92EXP.DAT
  100.0, 0.0,
 DMAP.BIN
  1, 1, 100, -100,
 DPEAKS.DAT

3 Controle_cards
  controle card description.

4 CC_1_Title    
	CC 1 -	TITLE
		FORMAT(80A1)

4 CC_2_Unit_Cell
	CC 2 -	cell parameters in angstroms and degrees.
		A,B,C,ALPHA,BETA,GAMMA
		FORMAT(6F10.4)

4 CC_3_S.F.InputFile
	CC 3 -	structure factor input file name
		FORMAT(40A1)
		
4 CC_4_MapInput
	CC 4 -	S.G.,MAPTYP,STHMN,STHMX,FOSCL,PAR1,PAR2
		S.G. - space group number (not used).
		MAPTYP =-1 , Straight copy (see note)
		       = 0 , Patterson map
		       = 1 , Fcal map
		       = 2 , Fobs map (phases from Fcal)
		       = 3 , 2*(Fo-Fc) map (phases from Fcal)
		       = 4 , 2Fo-Fc map (phases from Fcal)
		       = 5 , 3Fo-2Fc map (phases from Fcal)
		STHMN,STHMX - min. and max. sin(theta)/lambda 
				(1/(2d(max)),1/(2d(min)))
		FOSCL - scale factor to be applied to Fobs. 
	                     (Not used for MAPTYP=-1)
		PAR1,PAR2 - parameters transfered to expand for 
			    more complex maps. Not presently used.
		FORMAT(2I5,5F10.5)
		
4 CC_5_Orientation
	CC 5 -	map orientation.
		axis across, axis down, sectioning axis
		FORMAT(3A1)
		
4 CC_6_Sectioning
	CC 6 -	map sectioning
		MIN, MAX and NUMBER of grid points along A-axis.
		MIN, MAX and NUMBER of grid points along B-axis.
		MIN, MAX and NUMBER of grid points along C-axis.
		FORMAT(9I5)
		Note: MIN's may not be less than 0.
		      NUMBER's may not be greater than 128. 
		      Multiples of 2 and 3 are best.
		      
4 CC_7_SymFile
	CC 7 -	name of file containing equivalent positions.
		FORMAT(40A4)
		
4 CC_8_MapScale
	CC 8 -	MAPSCALE,F(000)
		MAPSCALE - scale factor to be applied to map.
		F(000) - estimate of F(000)
		FORMAT(2F10.5)
		
4 CC_9_MapFile
	CC 9 -	name of output map file
		FORMAT(40A1)
		Note: if blank the name MAP.TMP will be used.
		
4 CC_10_PeakData
	CC10 -	IFPOS,IFNEG,MINPOS,MAXNEG
		IFPOS = 0, No search for positive peaks.
		      = 1, Search for positive peaks.
		IFNEG - As IFPOS but for negative peaks.
		MINPOS - minimum value to be considered as positive peak.
		MAXNEG - Maximum value to be considered as negative peak.
		FORMAT(4I6)
		Note: If IFPOS=0 and IFNEG=0 no peak search is done.
		
4 CC_11_PeakFile
	CC11 -	Name of output peak file
		FORMAT(40A1)
		Note: if blank no file created.


2 Symmetery
 EQIVALENT POSITION CARDS.

3 Example
   Sample equivalent position cards for space group 92.
 =====================================================================
   8
   1  0  0  0  1  0  0  0  1  0  0  0
  -1  0  0  0 -1  0  0  0  1  0  0  6
   0  1  0 -1  0  0  0  0  1  6  6  3
   0 -1  0  1  0  0  0  0  1  6  6  9
   0  1  0  1  0  0  0  0 -1  0  0  0
   0 -1  0 -1  0  0  0  0 -1  0  0  6
  -1  0  0  0  1  0  0  0 -1  6  6  3
   1  0  0  0 -1  0  0  0 -1  6  6  9
 ========================================================================

3 Input
  Equivalent position card description.
 	C 1 -	Number of equivalent positions.
	C 2--	M1,M2,M3,M4,M5,M6,M7,M8,M9,T1,T2,T3
		FORMAT(9I3)
		(X')   (M1 M4 M7) (X) (T1/12)
		(Y') = (M2 M5 M8)*(Y)+(T2/12)
		(Z')   (M3 M6 M9) (Z) (T3/12)

2 Running

3 Example
 SAMPLE COMMAND FILE FOR RUNNING.
 =====================================================================
 $ SET DEF [QUIGLEY.HEXDAU]
 $ SET WORKING_SET/LIMIT=200
 $!
 $!
 $ TIM
 $ RUN [QUIGLEY.FOUR]FORIN
  D-CGTACG+Dau 
  27.92,27.92,52.89,90.0,90.0,90.0,0.0
 SFSNW.BIN
  92, 3, 0.0, 0.10, 1.00, 0.0, 0.0,
 BAC
  0,31,32, 0,31,32, 0,63,64,
 SG92EXP.DAT
  100.0, 0.0,
 DMAP.BIN
  1, 1, 20, -20,
 DPEAKS.DAT
 $ RUN [QUIGLEY.FOUR]EXPAND
 $ TYP EXPAND.OUT
 $ DEL EXPAND.DAT;*,EXPAND.OUT;*
 $ TIM
 $!
 $ RUN [QUIGLEY.FOUR]FFT
 $ TYP FFTOUT.DAT
 $ DEL FFTOUT.DAT;*,FFTIN.DAT;*
 $ TIM
 $!
 $!
 $! DEL EXPTMP.TMP;*
 $!
 $ RUN [QUIGLEY.FOUR]PEAKS
 $ TIM
 $! END
 $!
 $ LOG
 ================================================================

2 S.F.Input
 Note: Structure factor input.
 	Two forms of structure factor input are presently accepted
 depending on the type of map being calculated.
 Map type = -1 - Straight copy
 	S.F. file consists of IH,IK,IL,STHOL,A,B
 	      IH,IK,IL INTEGER*2
 	      STHOL,A,B REAL*4
 MAP TYPE = 0-5
	S.F. FILE IS IN M.I.T.Lab.of Mol.Structure PROLSQ input format.
	   IH,IK,IL,AC,BC,FO,SGFO,STHOL,(ASF(I),I=1,6)
	      IH,IK,IL INTEGER*2
	      AC,BC,FO,etc REAL*4

