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mmboxa

by Admin last modified 2008-10-30 08:21

derived from Judy Smith's NNBOX program but with more statistics suitable for more high resoution crystallographic analysis.

C  MMBOXA  derived from Judy Smith's NNBOX program but with more statistics
C         suitable for more high resoution crystallographic analysis.
C
C      VX 1.00  pre-1985        RH      from Judy's program NNBOX
C      VX 1.01  23-05-85        JMB     outer radius can be .GT. NXM1
C      VX 1.02  24-11-86        RH      last version before sincfit
C      VX 1.03  07-12-86        RH      sinc func fit over 4x4 box (trial)
C      VX 1.04  21-04-87        RH      sinc func fit over 2X2 box (better)
C      VX 1.05  10-06-87        RH      radius limits now in Angstroms.
C      VX 1.06  09-09-87        RH      more spots, 2000 now PARAMETER.
C      VX 1.07  18-06-92        RH      health warning if origin is given twice
C      VX 2.00  09-01-92        RH      brought to UNIX on Alliant - no changes.
C      VX 2.01  06-10-92        RH      extra dummy output column.
C      VX 2.02  17-04-95        RH      extra precision for scale factor output.
C      VX 2.03  19-07-95        RH      output opened UNKNOWN to allow overwrite
C      VX 2.04  22-04-96        RH      debug IPERIM -> perim
C      VX 3.00  29-11-97        RH      changed background definition -> MMBOXA
C      VX 3.01  29-03-00       JMS      irtorg mod to include zorigin
C      VX 3.02  29-10-01        RH      change filenames to CHARACTER*80
C   !!!  remember to put date and version # in title output record below.
C
C###############################################################################
C      NNBOX prints out amplitudes & phases in N * N boxes from a 
C      Fourier transform.
C
C  The change to MMBOXA on 29.11.97 was made to eliminate the effect that has 
C  been observed by those who have been applying a rather tight box to the 
C  image area (to select the best regions), which is that the number of "good" 
C  spots tends to increase as the area boxed decreases, but in a way which does 
C  not indicate better data (e.g. high IQ spots occur at ridiculously high 
C  resolution).  This was due to a different algorithm being used for peak and 
C  background in the calculation of the IQ value of the spots, such that when 
C  adjacent pixels in the transform are correlated, as occurs with images 
C  containing only a small boxed area, the ratio of peak to background increases
C  slightly giving an appearance of improvement where none actually occurs.  
C  This has been corrected from version 3.00 onwards by changing the background
C  calculation so that it uses the same algorithm as the peak.  The change has 
C  a very small effect on unboxed transforms but effectively eliminates the 
C  spurious spots on heavily boxed images with IQ values of 3 or even 2 where 
C  there is in reality only noise.  An additional fudge-factor of 1.10 has been
C  applied in the subroutine GET_RMSBK to make the signal-to noise ratio of 
C  spots with the same IQ-value identical to that used in earlier versions of
C  MMBOX on full-size unboxed images.
C
C  DATA:
C
C       FILIN
C
C       ISER,TITLE (I10,15A4)
C
C       GU     (A)
C
C       GENGRID(A)
C
C       GENPTS (A)
C
C       IPIXEL, IOUT,NUMSPOT, NOH, NOK, NHOR, NVERT  (*)
C
CHENN>
C       FILOUT only if IOUT.NE.0 .and. IOUT.NE.3
C
C       FILOUT2 only if IOUT.EQ.2 -> Statistics output file
C
C       FILOUT2 only if IOUT.EQ.3 -> Spotlist file
C
C       IQMAX only if IOUT.EQ.3 -> max value of IQ for inclusion in Spotlist
CHENN<
C
C       XORIG, YORIG  (*)
C
C       RINNER, ROUTER, IRAD, ACELL, BCELL, WIDTH, ABANG  (*)
C
C  if GENGRID :
C
C       AX, AY, BX, BY (*)
C
C  if .not. GENGRID :
C
C       IH(I), IK(I), X(I), Y(I)  (*)
C
C
C     ISER        serial number for run to be printed & output on IOUT.
C     TITLE       title to be printed & output on unit IOUT.
C     GU          if YES work in grid units, otherwise in mm.
C     GENGRID     if YES generate grid from lattice points (1,0) & (0,1)
C     GENPTS      if YES individual spots requested & generated from grid
C     IPIXEL      pixel size only used if .not.GU 
C     IOUT        output unit number for serial number and title, then
C                  IH,IK,A,P,IQ terminated with IH=100.
C     NUMSPOT     number of spots to be printed, if 0 defaults to 20.
C     NOH, NOK    number of orders of spots in H & K direcions
C     NHOR, NVERT box size in mm or grid units in horizontal &
C                 vertical directions,
C                 i.e. X & Y resp. ( up to 20 grid units in each
C                 direction).
C     XORIG, YORIG X & Y phase origin shifts to be added to those
C                  added to those read in on the transform
C     RINNER, ROUTER inner & outer radius in mm, grid units or Angstroms,
C                 within which spots (centre of box) must fall.
C     IRAD        if IRAD = 0 radii are specified in mm or grid units.
C                    IRAD = 1 radii are in Angstroms using a, b, gamma
C     ACELL
C     BCELL       cell dimensions, thickness (Angstroms)and cell angle gamma.
C     WIDTH             (used to calculate radii when IRAD = 1)
C     ABANG
C     AX,AY,BX,BY coordinates in mm or grid units of 1,0 & 0,1 spots
C                 respectively
C     IH, IK      indices of individual spot
C     X, Y        coordinates of individual spot.
C
C****************************************************************************

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