The 3d maps, fc1.6A.map and fc9A.map are Fcalc maps for
PDB entry 1A54

to look at peaks try on section 24 to section 24 with scale factor 100

./mapdump mapin fc1.6A.map 
24 24 100
GO

and

to look at peaks try on section 12 to section 12 with scale factor 100

./mapdump mapin fc9A.map 
12 12 100
GO


the above maps made from

sfall HKLIN   pbp.mtz\
      XYZIN   pdb1a54.ent\
      HKLOUT  sfall.mtz \
      << eof
TITLE  A197C_chromophore
GRID   60 80 160
RESO   100 1.6 
RSCB   100 1.6
RATI   3                 
BADD   0                 
MODE   SFCALC XYZIN HKLIN
LABIN   FP=F_pbp  SIGFP=SIGF_pbp
LABOUT  FC=FCALC PHIC=ACALC
END
eof
fft HKLIN   sfall.mtz \
    MAPOUT  fc.map \
    << eof
TITLE A197C_chromophore
RESOLUTION 100 1.6
SCALE F1 1.0 0.0               !  (SCALE1, TF1)
LABIN F1=F_pbp SIG1=SIGF_pbp PHI=ACALC
eof
extend MAPIN   fc.map \
       XYZIN   pdb1a54.ent\
       MAPOUT  fc1.6A.map\
       << eof
BORDER 5
eof
peakmax MAPIN  fc1.6A.map    << eof
NUMPEAKS 1000
THRESHOLD RMS 3.5 NEGATIVES
OUTPUT PEAKS
ORTH 1
eof
sort +1 -n PEAKS
highest peak 5.23 21 76 24



#-------------------------------------------------------------------
fft HKLIN   sfall.mtz \
    MAPOUT  fc.map \
    << eof
TITLE A197C_chromophore
RESOLUTION 100 9
SCALE F1 1.0 0.0               !  (SCALE1, TF1)
LABIN F1=F_pbp SIG1=SIGF_pbp PHI=ACALC
eof
extend MAPIN   fc.map \
       XYZIN   pdb1a54.ent\
       MAPOUT  fc9A.map\
       << eof
BORDER 5
eof
peakmax MAPIN  fc9A.map    << eof
NUMPEAKS 1000
THRESHOLD RMS 2.5 NEGATIVES
OUTPUT PEAKS
ORTH 1
eof
sort +1 -n PEAKS
highest peak 0.16  4  8 12