POSTREF (CCP4: Unsupported Program)

NAME

postref - Post-refinement of reflection data

SYNOPSIS

postref hklin foo_in.mtz hklout foo_out.mtz
[Key-worded input file]

DESCRIPTION

This program refines orientation and cell parameters for one or more rotation film packs, by comparing the intensities of partial reflections with a reference intensity.

KEY WORDED INPUT

Most cards are optional (except BATCH), and all are free format, with fields separated by 'space'. Cards may be in any order, except for BATCH and END. Any keyword may be abbreviated to 4 letters, and they are case-insensitive. Data for any card may be continued if necessary on the next line, by the character '-' or '&' at the end of the line.

The following keywords are available


       TITLE       ROCK          BEAM         MOSAICITY     SDFAC
       REFINE      CONSTRAINT    FIX          FREE          DELAY
       REJECT      RESOLUTION    PRINT        DEBUG         REFMEAN
       REFSUM      REFALL        WAVELENGTH   CELL          MISSET
       SCALE       OUTPUT        INSCALE      BATCH         CRYSTAL
       END

TITLE title

Title to write to printer output.

ROCK keyword(s)

Rocking curve keywords are STEP, COSINE (default) or TANH for square profile, cosine profile, or hyperbolic tangent profile respectively, and ISOTROPIC (default) or ANISOTROPIC for isotropic or anisotropic divergence refinement. If present, STEP, COSINE or TANH must precede ISOTROPIC or ANISOTROPIC.

ISOTROPIC is equivalent to

     FREE ET
     FIX  DH DV DL CD

ANISOTROPIC is equivalent to

 
     FREE DH DV
     FIX  ET DL CD

For the tanh profile, the TANH keyword may be followed by the keyword WTANH (alias LIMIT) and a value for the truncation limit WTANH ( = w in section following expression (c) above) which is used to make the tanh function into a bounded curve; and the keyword QTANH (alias SCALE) may be followed by a scale factor for the argument of the tanh function ( = q in expression (c) above): the refined value of the reflection width or divergence will be dependent on the value of w/q, since as w is increased, more of the tail of the profile is included in the reflection width. The default value of w = WTANH = 2.7 ( tanh(2.7) = 0.991 ), which means that the curve is truncated at Pcal = 0.0045 and Pcal = 0.9955. The default value of q = QTANH = 2.0

MOSAICITY <eta>

Specify crystal mosacity eta (degrees) to override value in file

BEAM [FILE] | [<DH> <DV> <DL> <CD>]

Define beam parameters to override values in file.

If the keyword FILE is given, the beam parameters and mosaicity will be picked up from the input file (from OSCGEN and ABSCALE) (this the default).

DH: horizontal beam divergence (degrees)
DV: vertical beam divergence (degrees)
DL: delta(lambda)/lambda = dispersion
CD: correlated component of the spectral dispersion

FIX or FREE followed by labels

Specifies which parameters are to be refined. The 2-character parameter labels are:

          A*, B*, C*   cell edges
 
          AA, BA, GA   cell angles
 
          WL           wavelength
 
          ZM, ZD       mean and difference of epsilon-z
 
          YM, YD       mean and difference of epsilon-y
 
          ET           mosaicity (eta)
 
          DH, DV       horizontal, vertical beam divergence

          DL           dispersion, delta lambda/lambda (leave fixed)

          CD           correlated dispersion (leave fixed)

The keywords FIX or FREE may be mixed with parameter labels to specify the status of subsequent parameters given on the card.

Defaults: cell parameters normally default to the flags given in the orientation block, but if any cell parameter label is given here, all the cell parameters will default to free. The cell flags in the file also indicate constraints tying cell edges together (eg a* = b* ): these constraints are not affected by FIX or FREE cards. Other parameters are by default fixed except for ZM, YM and ET (or DH & DV if the divergence is anisotropic: a ROCK ... ANISOTROPIC card sets DH & DV free and fixes ET). If WL is free, the cell edges A*, B* and C* are automatically fixed. You would be ill-advised (probably) to refine beam parameters other than ET or DH+DV.

DELAY label delay ....

This card takes a series of pairs of parameter-label, 'LABEL', (see FIX card) and a number DELAY, which makes that parameter fixed for the first DELAY cycles, after which it reverts to its staus as defined by FIX and FREE cards. All delays default to zero.

CONSTRAINT icon(1) ... icon(6)

Set cell constraint flags to override those derived from the input file. If ICON(I) = J, the I'th cell dimension is constrained to equal the J'th: normal values are 1 2 3 4 5 6 .

REFINE ncyc convrg fltlim fltstt fltdec

NCYC is the number of cycles (defaults to 8).

CONVRG is a convergence limit (default = 0.02); the refinement has converged if the change of SIG = Sqrt ( Sum ( w del**2 ) ) / (Nobs - Npar) is less than CONVRG.

FLTLIM, FLTSTT, FLTDEC. The filter-level is the amount added to all eigenvalues to speed convergence: it has the effect of damping shifts in the directions corresponding to small eigenvalues. The filter level starts at FLTSTT, and is decremented by FLTDEC until it reaches FLTLIM (defaults 0.0,0.05,0.02)

REJECT fincr rejfac(1) rejfac(2) cutoff rejang frlow frdec rejsd frclim

Reflection rejection limits etc.

FINCR
Intensity increment for analysis against intensity (default = 1000). Used only when PRINT is set to ANALYSIS or FULL. Max. no. of bins fixed at 12.
REJFAC(1)
reject reflections with Iobs < REJFAC(1) * sd(Iobs) (default = 0) The refinement seems to converge best with all data included.
REJFAC(2)
reject reflections with Iref < REJFAC(2) * sd(Iref) (default = 0)
CUTOFF
reject reflections with sd(fraction obs) > CUTOFF (default=0.5)
REJANG
reject reflection closer than REJANG degrees to the rotation axis on the film (default = 3 degrees)
FRLOW,FRDEC
define which non-fractional reflections are used. In each cycle, reflections are used with calculated fraction Pcal such that
         -FRL < Pcal < 1 + FRL
FRL starts at FRLOW on the first cycle, and is decremented by FRDEC on each cycle until FRL = 0.0. This allows reflections which are just outside the fractional range to be used in the early cycles, in case they are really fractional. These reflections are weighted by
 
      (1 - exp( - (delta I)**2/2(sd(I))**2 ) )
to weight down those reflections which are really non-fractional. (Defaults 0.0, 0.0)
REJSD
reject reflections for which Pobs - Pcal > REJSD * sd(Pobs) (default = 10.0)
FRCLIM
omit reflections altogether from calculation if the calculated fraction in the input file FRACTIONCALC is greater than FRCLIM. If this fraction is reliable, leaving out the safe fully recorded reflections speeds up the calculation considerably.

REFMEAN

Use mean of safe fully recorded reflections (IMEAN) as reference intensity (default, cards REFSUM and REFALL are alternatives).

REFSUM

Use summed partials (ISUM) as reference intensity.

REFALL

Use summed partials (ISUM) as reference intensity if present, otherwise IMEAN

RESOLUTION res1 [res2]

RES1,RES2. Set resolution limits in Angstrom, either order. If only one number given, use as high resolution limit. Default, use all data.

SDFAC sdfac sdadd

Read modification factors for standard deviation of Iobs, as for ROTAVATA and AGROVATA.

Variance(Iobs):= SDFAC**2 ( Var(Iobs) + (SDADD * Iobs)**2 )

(Default 1.0, 0.0 ie no change)

CELL a b c [alpha beta gamma]

Read real cell dimensions (Angstrom and degrees) to override those on the file. Angles default to 90. This needs to be repeated for each CRYSTAL card.

WAVELENGTH wavelength

WAVELENGTH is the wavelength in Angstrom to override value in file. If this card is present but no value is given, the wavelength is set to 1.54182 (Cu Kalpha). This needs to be repeated for each CRYSTAL card.

MISSET phix phiy phiz [phix2 phiy2 phiz2]

Read mis-setting angles (degrees) to override those in the file. Two different sets of three angles may be specified, corresponding to the start and finish of the rotation range (phi1 and phi2). By default, the two sets are equal (ie no crystal slippage). This needs to be repeated for each CRYSTAL card.

SCALE scale bfac

Read scale and temperature factor for the next batch, to override the values in the file. If this card is present, the next BATCH card must specify one batch only.

OUTPUT [keyword]

The keyword OFF switches off output of reflections to the output MTZ file. The keyword ALL makes the program copy all batches to the output file, even if they are not refined. An OUTPUT card with no keyword resets the default option, to write to the output file only those batches which are refined.

INSCALE [keyword]

By default, a scale correction is applied if a column SCALE is present in the file. The INSCALE card switches the application of this scale off or on again. Keywords OFF or ON may be present, otherwise the card switches to the opposite state

PRINT keyword

Set amount of analysis etc printed. The optional keywords are:

BRIEF
(default) minimal output, prints only the analysis against fraction
SHIFTS
(or PRINT with no keyword) prints also the shifts on EACH cycle and the orientation data from the header records for each batch.
ANALYSIS
additional extensive analysis after the last cycle (this is worth doing for at least a few films).
FULL
is equivalent to both SHIFTS and ANALYSIS
REFLECTIONS
in addition to the FULL analysis, all reflections are printed on the last cycle.
VECTORS
prints eigenvectors of normal matrix on last cycle, as well as eigenvalues.

DEBUG ibug

Set debug flag to give extensive (!) output for debugging.

BATCH [ batch-specification ]

This card is an alternative to the CRYSTAL card, specifies which batches are to be refined as independent films, and refines them. Note that unlike other cards which specify parameters or flags, the BATCH card tells the program to refine the specified batches, after which further cards are read to change parameters and refine more batches if required. Batches must always be specified in the order they occur in the file, ie in ascending order of batch number.

Specification of batches

(a)
ALL all batches (default if no keyword on BATCH card)
(b)
list of batches n1 n2 n3 etc
(c)
range of batches n1 TO n2
(d)
EXCLUDE with list n1 n2 n3 etc This may follow ALL or a range.

CRYSTAL [keywords] batch-specification

This card is an alternative to BATCH, and specifies a group of films to be refined together (up to 50). The batch specifications are the same as for the BATCH card. By default, mis-setting angles and rocking curve parameters are refined independently for each film. The keyword ONEMISSET causes the same set of mis-setting angles to be refined for all files, and the keyword ONEROCK the same set of rocking curve parameters. Both keywords may be present. Note that the ONEMISSET option will not work well with a set of films covering a large rotation angle, since the refinement of misseting within each cycle is done in the camera frame rather than the crystal frame.

END

This terminates the program. Alternatively, the program ends on end-of-file on stream 5. If OUTPUT ALL was specified, any remaining unrefined batches in the file are copied to the output file.

INPUT AND OUTPUT FILES

Input Files

The control data file
HKLIN The input reflection data file. This is a multi-record MTZ file (See section PROGRAM FUNCTION for details)

Output Files

HKLOUT The output reflection data file. This is a multi-record MTZ file (See section PROGRAM FUNCTION for details)

PRINTER OUTPUT

Comments on the printer output

Definitions of statistics:

Avdel = 1/n Sum  delta I
 
Avsd  = 1/n Sum sqrt(1/weight)
 
rmsdel= sqrt( 1/n Sum(delta I **2) )
 
rmsesd= sqrt( 1/n Sum(1/weight) )
 
      = sqrt( 1/n Sum( Var(Iobs)) )
 
RDEL    = Rfactor = Sum  Icorr - Iref  / Sum  Iref
 
RSIG    = fractional mean sd(Icorr-Iref)
 
        = Sum{sqrt[Var(Iobs)/(Pcal**2) + Var(Iref)]} / Sum Iref
 
RDEL and RSIG exclude reflections with Pcal < 0.1
 
DPER    = weighted mean delta(fraction)
 
        = Sum[(Pobs - Pcal)/Var(Pobs)] / Sum[1/Var(Pobs)]
 
ADPER   = weighted mean  delta(fraction)
 
        = Sum[ Pobs - Pcal /Var(Pobs)] / Sum[1/Var(Pobs)]
 
ESD     = rms sd(fraction) = sqrt[Sum Var(Pobs)/n]
 
RMS     = rms delta(fraction) = sqrt[Sum(Pobs-Pcal)**2/n]
 
Q = S/NR = mean delta(fraction)**2/variance
 
         = 1/n Sum[(Pobs-Pcal)**2 / Var(Pobs)]
 
For all statistics, Pcal = 1 for a fully recorded reflection,
 
                         = 0 for a non-recorded one.

ERROR MESSAGES

Data control card errors

!!!! Keyword KEY not recognised !!!!
 
!!!! Syntax error on card !!!!
 
!!!!!! Unrecognised parameter label: LABEL         (FIX/FREE/DELAY)
 
!!!! Scale card is only valid with one batch specified on card !!!!
 
Errors in opening units
 
STOP **UNABLE TO OPEN UNIT 5 OR 6**
 
STOP **UNABLE TO OPEN UNIT 9**
 
Too many parameters
 
!!!!! Too many free parameters, maximum is N
 
Problems with the Batch Handling
 
!!!! Too many batches in list: N
 
!!!!! No orientation data found for batch N
 
!!!!! Too many films for this crystal, maximum = N
 
NB batch N has no reflections contributing to refinement !!!!
 
**** Batch number not found in file ****
 
!!! Error in batch titles in NEWFIL !!!
 
Point Group dictionary
 
Point group PG not found in library !!!!
 
!!!!!!! Warning: point group name was previously set to PG !!!!!!!!
 
Matrix handling
 
!!!!!! Symmetry matrix is singular !!!!!!
 
MTZ file errors
 
!!!!! First five columns of input file are out of order Nq1 N2 N3 N4 N5
 
Error on reading MTZ file: Error no. N

Error messages may also be produced by the MTZ file handling routines. These start with the message **MTZ ERROR** and are documented elsewhere.

PROGRAM FUNCTION

This program is based on the post-refinement program by Winkler and Schutt (ref. 1). It refines orientation and cell parameters for one or more rotation film packs, by comparing the intensities of partial reflections with a reference intensity. The reference intensity is typically the mean of safe fully recorded reflections from the same or different films, or the sum of the spot with its other half. The reference intensity and the appropriate scale factor may be provided by the program ROTAVATA.

The residual minimized is


           Sum w ( Iobs - Pcal Iref )**2

where the calculated fraction Pcal is a function of the following parameters:

Cell dimensions
Wavelength (as an alternative to cell edges)
Misorientation angles phi-z, phi-y, phi-x (optionally different at the two ends of the rotation range). Within each cycle the program refines the mis-setting angles in the camera frame epsilon-z and epsilon-y (ZM and YM), and optionally their difference ZD and YD, then rotates the epsilon shifts into the reference frame (phi-z, phi-y, phi-x ) after each cycle.
Rocking curve parameters (divergence and dispersion)

The program may refine each film pack (batch) seperately, or a group of films (up to 50) may be refined together with the same cell dimensions, with the same or different mis-setting angles and rocking curve parameters (see CRYSTAL card).

The program allows three alternative forms of rocking curve to relate the angular fraction to the intensity fraction: both have a finite angular width 2g, such that the intensity fraction


          Pcal = 1/2 ( 1 +- f(b) )

where b is the angular fraction (ie fraction of g) = delta beta / g


      (a) square profile   f(b) = b
 
      (b) cosine profile   f(b) = sin ( b * pi/2 )
 
      (c) hyperbolic tangent profile f(b) = tanh ( q * b )
 
          where q = QTANH is a scale for the tanh function (see ROCK card).

Note that function (b) is defined only for -1 < b < 1 and (c) for b < (w/q): otherwise function (a) is used. The tanh function (c) is equivalent to a peak with tails compared to the cosine function. For the tanh profile, b = (w/q)*(delta beta / g ), and b is truncated at b = w/q : w = WTANH is the truncation limit (see ROCK card). This scaling ( parameters w and q ) makes the divergence for the tanh function more comparable with that for the cosine curve.

The reflection width g includes a dispersion term, and may be anisotropic.

 
   g = 1/2 * ( sqrt( (2  TANtheta  *  CD  +  DH  COSalpha)**2  +  (DV  *
       SINalpha)**2) + ET + DL * TANtheta )

see Greenhough & Helliwell (ref. 2) and Greenhough (ref. 3) (see BEAM card) where alpha = (tan)**-1 y/z , the azimuthal angle on the film. Note that g is the half-width of the reflection, but the rocking-curve parameters ET, DH & DV refer to the full-width of the reflection.

A note on convergence

If the program is refining parameters for one film at a time, some parameters are poorly determined. This may not be too serious, since we are not interested in the parameters themselves, but only in the fractionality calculated for each reflection from the parameters. In particular, the mis-setting angle about the rotation axis phi-z (epsilon-z) is correlated with the cell dimensions perpendicular to the rotation axis. Cell angles are even more correlated, and it is doubtful whether cell angles can be refined sensibly with only one film. The program has three facilities which may assist convergence.

a): Eigenvalue filtering (see REFINE card)
A number (filter) may be added to all eigenvalues of the normal matrix during the calculation of shifts. This is equivalent to adding the filter value to all diagonal elements of the normal matrix (Marquardt method), and has the effect of damping shifts in the direction corresponding to the smallest eigenvalues. The filtering seems useful on the first few cycles, to allow the most sensitive parameters to refine first, but it is best decremented to zero after 3 or 4 cycles (as is done in the default settings).
b): Parameter delay (see DELAY card)
Any parameter may be fixed for the first few cycles. This may be useful for the parameters ZD and YD, which define the difference of orientation at the beginning and end of the rotation range.
c): Inclusion of reflections which are not partial, but are nearly so. (parameters FRLOW and FRDEC on REJECT card)
It is possible to include reflections bordering on the partial in the early cycles, since they may become partial as the parameters change. This seems not to be helpful, but may be in some cases

Details of input reflection file

The input MTZ file may be prepared by ROTAVATA and SORTMTZ. It contains a series of films (batches) which are processed sequentially, although individual batches may be selected for inclusion or exclusion. The file must be sorted with BATCH as the most significant key. The file is expected to contain columns

H K L M/ISYM BATCH I SIGI FRACTIONCALC IMEAN SIGIMEAN ISUM SIGISUM

where IMEAN and ISUM are alternative reference intensities, respectively the mean of the safe fully recorded reflections, and the sum of the two adjacent partials.

The file should also a batch header and orientation block for each batch. The orientation block contains starting values of the orientation parameters, constraint flags for cell parameters, and the relative scale and temperature factor (from ROTAVATA) to put this batch on the same scale as the reference intensity. The orientation blocks are put into the file by ABSCALE. The orientation parameters in the file may be overridden by control data (see above).

Orientation data (see also libmtz.doc)


       1.  6 cell dimensions (Angstrom and degrees,  real  numbers).  These
           cell dimensions define an orthogonalization matrix B to  convert
           indices hkl to Cartesian crystal axes xyz
 
           x  =  B  h
 
           B = (a*        b* cos gamma*    c* cos beta*            )
               (0         b* sin gamma*   -c* sin beta* cos alpha  )
               (0               0             lambda / c           )

                                               (Busing & Levy 1967)
 
           This gives x parallel to a*, and y in the a* b* plane.
 
       2.  6 cell dimension flags (integer) defining which parameters may
           be varied.
 
               Flag = -1       parameter is freely variable
 
                    =  0       parameter is fixed (ie cell angle  =  90  or
                               120)
 
                    = I(.gt.0) parameter is constrained to  have  the  same
                                value as parameter number I .
 
       3.  Orthonormal matrix U (9 real numbers in order U11, U12, U13, U21
           etc) to rotate the crystal Cartesian coordinates to  the  camera
           Cartesian coordinates. The IDXREF matrix is A = U B . The matrix
           U defines a standard orientation,  and  is  a  function  of  the
           mounting axis and the axis defined as phi = 0 , but  it  is  not
           dependent on the misorientation angles. Typically, U will  be  a
           permutation matrix.
 
       4.  JUMPAX, the 'mounting' axis, as defined for  OSCGEN  (1,2,3  for
           h,k,l) (not used)
 
       5.  6 misorientation angles, rotation  axis  mis-setting  (6
           real numbers):
 
                 PHIX1 , PHIY1 , PHIZ1 , PHIX2 , PHIY2 , PHIZ2 
 
           The first three refer to the orientation at the beginning of the
           rotation range (at phistart), the second three  phi  angles  (if
           present) refer to to the end of the rotation range (at  phiend).
           The second set should be set  equal  to  the  first  set  if  no
           crystal slippage is assumed.
 
       6.  Start and stop rotation angles.  (  2  real  numbers)  phistart,
           phiend
 
       7.  crystal mosaicity in degrees 
 
       8.  lambda, delta lambda/lambda, correlated dispersion
 
       9.  Scale , Temperature factors for this batch ( from Rotavata etc).
           The correction to be applied is
 
                 SC * exp ( -2 * B * (sin theta/lambda)**2 )

Details of output reflection file

The output MTZ file is similar in structure to the input file. The refined orientation parameters are placed in the orientation block. For each reflection, the calculated fraction and its standard deviation are placed in columns labelled FRACTIONCALC and SIGFRACTCALC, and the partial flag M is updated (in column M/ISYM). Valid values of M are:


                   M = 0  fully recorded
 
                     = 1  partial ( 0  =< P < 1.0 )
 
                     = 2  not recorded ( P < 0 )
 
                     = 3  partial at both ends of the range
 
                     = 4  too near axis (see REJANG above on REJECT) card

Reflections with M > 1 will be rejected in AGROVATA.

REFERENCES

Winkler F.K., Schutt C.E. & Harrison S.C., Acta Cryst., (1979), A35, 901 - 911.
Greenhough T.J. & Helliwell J.R., J. Appl. Cryst., (1982), 15, 493 - 508
Greenhough T.J., CCP4 Information Quarterly for Protein Crystallography, Feb. 1983, Daresbury Laboratory.

AUTHORS

Originator : Winkler and Schutt
Availability : Fortran77/vms/unix
Contact : Phil Evans, MRC Cambridge

EXAMPLES

Example 1.


!
! Sort output file from Rotavata for postrefinement
!
$SORTMTZ HKLIN RPFKPRF2 HKLOUT RPFKPRF2S BATCH H K L M/ISYM
!
! Now postrefine
!
$POSTREF HKLIN RPFKPRF2S HKLOUT RPFKPRFT6
TITLE PFK R-native, 2nd postrefine rescaled, averaged cell, tanh 2.3
POINTGROUP PG222
FREE WL
FIX A* B* C* AA BA GA
REFINE 20 0.01 0.0 0.05 0.02
ROCK TANH LIMIT 2.3
REJECT 1000 0 0 0.5 10 
CELL 122.17 84.30 61.26
BATCH 200 TO 299
CELL 122.84 84.39 61.60
BATCH 300 TO 399
CELL 122.67 84.39 61.53
BATCH 400 TO 499
CELL 122.67 84.20 61.59
BATCH 500 TO 599
CELL 122.77 84.10 61.86
BATCH 600 TO 699
CELL 122.70 84.64 61.52
BATCH 700 TO 799
!
! Resort data ready for Agrovata or Rotavata
!
$SORT: SORTMTZ HKLIN RPFKPRFT6 HKLOUT RPFKPFTS6 H K L M/ISYM BATCH

Example 2.


$SORTMTZ HKLIN ROTSTR3 HKLOUT ROTSORT BATCH H K L M/ISYM
$POSTREF HKLIN ROTSORT HKLOUT PREFSTR2
TITLE STR-ATP C* POSTREF
POINTGROUP PG222
ROCK TANH LIMIT 2.5
CRYSTAL ONEROCK 1391 TO 1394
CRYSTAL ONEROCK 1501 TO 1504
CRYSTAL ONEROCK 1521 TO 1524
CRYSTAL ONEROCK 1531 TO 1535
CRYSTAL ONEROCK 1541 TO 1543
CRYSTAL ONEROCK 1545 TO 1548
CRYSTAL ONEROCK 1551 TO 1555
CRYSTAL ONEROCK 1561 TO 1564
CRYSTAL ONEROCK 1567 TO 1569
END
.

Example 3.


#!/bin/csh -f
#
#  Recycle Rotavata & Postref
#
# Number of cycles controlled by parameters in next few lines
#   To do final merge, set cycle = maxcycle
#
cd $scr0
set dataset = bst
set cycle = 3
set nextcycle = $cycle           # For final merging only: else reset below
set maxcycle = 3
set saved = /ss1/pre/pfk/bst

# Following line to do final merge
if ($cycle == $maxcycle && $cycle != 1) then
 goto agro
endif


#  Skip initial Rotavata if restarting after cycle 1

if ($cycle == 1) then

rotavata  hklin  ${saved}/${dataset}_sort  
   hklout ${dataset}_save_${cycle}  
          scales  ${dataset}_${cycle}.scales << end_rota
title BST PFK T9 + T10
batches 100
bins    10
brefine on
cycles  5
scale unity
output  postref
resolution 20 2.6
rejlim 4
width  1500
intensities  profile
process  full  partial
sdinflate  sdfac = 1 sdadd = 0.04
anomalous off
records  truncate
end_rota

endif

########### Return here for next cycle
cycle:
echo =============================================================
echo 
echo    Postrefinement cycle $cycle 
echo 
echo =============================================================

@ nextcycle = $cycle + 1

#  Sort for Postref on BATCH
#
sortmtz hklin  ${dataset}_save_${cycle} 
        hklout ${dataset}_prfrs_${cycle} << eof-sort
BATCH H K L M/ISYM
eof-sort

postref:
postref hklin  ${dataset}_prfrs_${cycle} 
        hklout ${dataset}_savep_${cycle} 
 summary ${saved}/${dataset}_${cycle}.prfsum << eof-prf
Title  PFK B.st T-state crystals  T9 & T10 cycle ${cycle}
rock tanh limit 2.3 isotropic
crystal 900 to 944
crystal 1000 to 1042
eof-prf

# Resort for Rotavata
#
sortmtz hklin  ${dataset}_savep_${cycle} 
        hklout ${dataset}_prfs_${cycle} << eof-s1
H K L M/ISYM BATCH
eof-s1

rota:
rotavata  hklin  ${dataset}_prfs_${cycle}  
   hklout ${dataset}_save_${nextcycle}  
          scales  ${saved}/${dataset}_${cycle}.scales << end_rota
title BST PFK T9 + T10
batches 100
bins    10
brefine on
cycles  5
scale postref
output  postref
resolution 20 2.6
rejlim 4
width  1500
intensities  profile
process  full  partial
sdinflate  sdfac = 1 sdadd = 0.04
anomalous off
records  truncate
end_rota

end_cycle:
# Clean up unwanted files
 /bin/rm ${dataset}_prf*

# Recycle if required

if ($cycle < $maxcycle) then
 @ cycle = $cycle + 1
 goto cycle
endif


time

##exit


##############################################################
#
#  Final merging
#

agro:

agrovata  hklin ${dataset}_save_${nextcycle}  
                hklout ${saved}/${dataset}_merge <<end-agro
@${saved}/${dataset}_${cycle}.scales
intensities profile
process full partial all
frmin 0.7
end-agro
#
exit

time

trunc:
truncate  hklin  ${saved}/${dataset}_merge 
          hklout ${saved}/${dataset}_F <<EOF-trunc
title BST PFK T9 + T10
wilson
#resolution  
nresidue   1280
labout  F=FT SIGF=SIGFT
EOF-trunc


time

Example 4:


#!/bin/csh -f
#
#  Postrefinement
#
#
#  First resort data on batch
sortmtz hklin $scr0/cx88_scl1 hklout $scr0/bc93_s << eof-1
BATCH  H K L M/ISYM
eof-1

# now for Postref
postref hklin $scr0/bc93_s hklout $scr0/bc93_p << eof-2
Title  Postrefinement B.st. PFK C2

rock   tanh  isotropic
!beam 0.03 0.01
refine 6
refall
sdfac  0.8 0.08
crystal  61   to  699
crystal  701  to  799
crystal  811  to  899
crystal  911  to  999
crystal 1111  to 1199
crystal onemisset 1311  to 1319
crystal 1321  to 1399
crystat 2011  to 2099
crystal 2111  to 2199
eof-2
#

#
# exit
#

# sort back for Rotavata
sortmtz hklin $scr0/bc93_p hklout $scr0/bc93_post << eof-3
H K L M/ISYM BATCH
eof-3