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Electron Density Map File

The output file of the xrefin map statement contains information about the unit cell, indexing of the map, and the actual electron density map. It can be read by a modified version of MAPPAGE to provide a “DSN6” file for FRODO. Modified versions of this program are included in the directory “[.VAX.FRODOMAP]" for the VAX/VMS system and “sgi/fft" for the SGI systems. The grid size of the map is determined by the GRID parameter in the FFT statement. The following is a FORTRAN example of how to read the formatted (QFORM=.TRUE.) or unformatted (QFORM=.FALSE.) version of the electron density maps:

C
C read title
      IF (QFORM) THEN
      READ(UNIT,'(/I8)',END=6,ERR=7) NTITLE
      IF (NTITLE .LE. 0) THEN
      READ( UNIT, '(A)',END=6,ERR=7) 
      ELSE
      DO J = 1, NTITLE
      TITLE(J) = ' '
      READ (UNIT, '(A)',END=6,ERR=7) TITLE(J)
      ENDDO
      ENDIF
      ELSE 
      DO J=1,MXTITL
      TITLE(J)=' '
      END DO
      READ(UNIT,END=6,ERR=7) NTITLE,(TITLE(J)(1:80),J=1,NTITLE)
      END IF
C
C read sectioning information
      IF (QFORM) THEN
      READ(U,'(9I8)',END=6,ERR=7)
     &  NA,AMIN,AMAX,NB,BMIN,BMAX,NC,CMIN,CMAX
      ELSE
      READ(U,END=6,ERR=7)
     &  NA,AMIN,AMAX,NB,BMIN,BMAX,NC,CMIN,CMAX
      END IF
C
C read unit cell constants in angstroms and degrees
      IF (QFORM) THEN
      READ(U,'(6E12.5)',END=6,ERR=7) (CELL(I),I=1,6)
      ELSE 
      READ(U,END=6,ERR=7) (CELL(I),I=1,6)
      END IF
      END IF
C
C read matrix mode
      IF (QFORM) THEN
      READ(U,'(3A)',END=6,ERR=7) MODE 
      ELSE
      READ(U,END=6,ERR=7) MODE 
      END IF
      IF (MODE.NE.'ZYX') THEN 
      CALL WRNDIE(-5,'RMAP','error in matrix mode')
      GOTO 7
      END IF 
C           
C read density matrix, c is slowest ("z-sections"). 
      DO C=CMIN,CMAX
C
C read next section
      IF (QFORM) THEN
      READ(U,'(I8)',END=6,ERR=7) KSECT
      READ(U,'(6E12.5)',END=6,ERR=7)
     &  ((MAP(A,B,C),A=AMIN,AMAX),B=BMIN,BMAX)
      ELSE
      READ(U,END=6,ERR=7) KSECT
      READ(U,END=6,ERR=7)
     &  ((MAP(A,B,C),A=AMIN,AMAX),B=BMIN,BMAX)
      END IF
      END DO

The following lines show the beginning of a typical electron density map file:

       2 !NTITLE
 REMARKS FILENAME=""                                                                                                                          
 REMARKS DATE:18-Jun-90  12:24:08       created by user:                                                                            
 XMAP: extend NA=(  30   4  12) NB=(  15   5  10) NC=(  16   2  12) 
      30       4      12      15       5      10      16       2      12
 XMAP: a= 40.96, b= 18.65, c= 22.52, alpha= 90.00, beta= 90.77, gamma= 90.00
 0.40960E+02 0.18650E+02 0.22520E+02 0.90000E+02 0.90770E+02 0.90000E+02
 XMAP: written in ZYX mode (z-sections)
ZYX
 XMAP: section #   0 average density=-0.336     sigma= 0.907    
       0
-0.97086E+00-0.49927E+00-0.82774E+00-0.13491E+01-0.57034E+00-0.71253E-01
-0.19491E+00 0.61017E+00 0.10064E+01-0.22888E+01-0.94020E+00 0.77451E+00
 0.57539E+00-0.31211E-01-0.27430E+00-0.36526E+00 0.34772E+00 0.81884E+00
-0.19954E+01-0.10117E+01 0.18038E+01 0.19008E+01 0.11886E+00-0.41646E+00
 0.47560E-01 0.48855E+00 0.57606E+00-0.22320E+00-0.12787E+01 0.47590E+00

Xplor-NIH 2024-09-13