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maketran

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

This program reads in an MTZ file of diffraction amplitudes and phases from the experimentally determined and merged 3-D data from a 2-dimensional crystal, and writes out the transform of the projection of the structure in the direction, at the magnification, and modified by the requested CTF, for later use as a reference in cross-correlation with the digitised experimental image.

C   MAKETRAN:  remember also to change version number in first write statement.
C
C   This program reads in an MTZ file of diffraction amplitudes and phases from
C       the experimentally determined and merged 3-D data from a 2-dimensional 
C       crystal, and writes out the transform of the projection of the 
C       structure in the direction, at the magnification, and modified 
C       by the requested CTF, for later use as a reference in cross-correlation
C       with the digitised experimental image.  The code is derived from a
C       synthesis of bits of ORIGTILT, MASKTRAN, CTFAPPLY & EDMTZ.
C
C       Version 1.00    1.9.94          RH      Original version
C       Version 1.01    9.9.94          RH      Temperature factor added
C       Version 1.02    4.12.94         RH      no STANG in p2
C       Version 1.03    6.5.95          RH      slight extrapolation of lattice line
C       Version 1.04    25.7.95         RH      set ASTAR, BSTAR in subroutines
C       Version 1.05    22.4.96         RH      add RH ASTAR, BSTAR changes
C       Version 1.06    4.7.99          RH      IBEGIN(-MAXINDEX:MAXINDEX,etc), etc
C       Version 1.07    29.03.00        JMS     zorigin inserted in ialorg for 
C                                                 compatibility with imsubs2000
C       Version 1.08    29.10.01        RH      change NAME to CHARACTER*80
C       Version 1.09    4.8.02          RH      check array bounds IBEGIN,IFINISH
C
C   Input cards: 
C
C   CARD 1 : NPROG,ISHAPE,IAMPLIM,RAD
C   CARD 2 : NX NY DSTEP XMAG
CHENN>
CC   CARD 3 : AX,AY,BX,BY,  REVHK,SGNXCH,ROT180
C   CARD 3 : AX,AY,BX,BY,  REVHK,SGNXCH,ROT180,ROT90,REVHND
CHENN<
C   CARD 4 : OX OY TX TY   TAXA TANGL A B GAMMA
C   CARD 5 : RESMIN RESMAX     resolution limits to be used in Angstroms
C   CARD 6 : DFMID1 DFMID2 ANGAST CS KV
C   CARD 7 : Output transform file name - mapformat, MODE=4 (complex reals)
C   CARD 8 : Output transform title to be put in image header.
C
C        Parameters describing reference data - MTZ format - SUBROUTINE GETSFS.
C   CARD 9 : ISPGRP,LFPZERO,SFACTOR,BFACTOR
C   CARD 10: LABIN F=AMP PHS=PHASE FOM=FOM ##   - 
C
C         NPROG   - 0 for 2-D crystals
C                 - 1 possible extensions to helical, icosahedral & single part.
C         ISHAPE  -    1 hard edge circular holes
C                      2 soft edge circular (Gaussian weight exp(-2) at edge)
C                      3 hard edge square holes 
C         IAMPLIM -  T, limit spot amplitude to 2x average spot amplitude
C                    F, no amplitude reduction
C         RAD     - radius of circular hole or half-dege length of square hole
C         NX      - Size of densitometered array (e.g. 2048 x 2048)
C         NY      -
C         DSTEP   - Densitometer step-size in microns.
C         XMAG    - Precise magnification normally worked out from lattice
C                    parameters and known cell dimensions.
C         AX,AY   - Lattice parameters (from MMBOX) of (1,0) and (0,1)
C         BX,BY   -                                     in grid units.
C         SGNXCH  - IF NOT EQUAL TO 0, FLIP AROUND A AXIS, USEFUL IN P121
C         ROT180  - IF NOT=0, ROTATE 180 DEG ABOUT Z-AXIS, USEFUL IN P1,P3
C         ROT90  - IF NOT=0, ROTATE 90  DEG ABOUT Z-AXIS, USEFUL IN P2221
C                  THIS IS A COSMETIC FEATURE TO FACILITATE INDEXING
C                  DIFFICULT HIGHLY TILTED FILMS. NOTE THAT ALL OTHER
C                  PARAMETERS, SUCH AS TAXA,TANGL MUST REMAIN CORRECT
C                  W.R.T. THE ORIGINAL DIRECTIONS FOR H AND K.
C         REVHND - IF NOT = 0, sign of Z is inverted.
C                  THIS IS A COSMETIC FEATURE TO FACILITATE debugging the
C                  damned handedness.
C                  NOTE THAT ALL OTHER
C                  PARAMETERS, SUCH AS TAXA,TANGL MUST REMAIN CORRECT
C                  W.R.T. THE ORIGINAL DIRECTIONS FOR H AND K.
C         REVHK   - IF NOT = 0, H AND K ARE INTERCHANGED ON INPUT.
C                         THIS IS A COSMETIC FEATURE TO FACILITATE INDEXING
C                         DIFFICULT HIGHLY TILTED FILMS. NOTE THAT ALL OTHER
C                         PARAMETERS, SUCH AS TAXA,TANGL MUST REMAIN CORRECT
C                         W.R.T. THE ORIGINAL DIRECTIONS FOR H AND K.
C         OX,OY   - origin in degrees for (1,0) & (0,1)
C         TX,TY   - beamtilt in milliradians for (1,0) & (0,1)
C         TAXA    - Angle measured from the tilt axis to the A-axis,
C                   measured in direction of A to B being positive.
C         TANGL   - tilt angle in degrees
C         A       - cell dimensions and space group angle.
C         B       -   "
C         GAMMA   -   "
C         RESMIN,RESMAX  -   resolution limits to be used in Angstroms
C         DFMID1  - Defocus level (underfocus +ve). If DFMID2=DFMID1, image
C         DFMID2  -  is non-astigmatic. Otherwise, amount of defocus in two
C                    orthogonal directions, DFMID1 being defocus in direction
C                    ANGAST (degs) relative to X and Y of the Fourier transform.
C         CS      - Sperical aberration in mm.
C         KV      - Accelerating voltage in kilovolts
C
C*******************************************************************************
C


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