
POSTREF (CCP4: Unsupported Program)
NAME
postref
 Postrefinement of reflection data
SYNOPSIS
postref hklin
foo_in.mtz
hklout
foo_out.mtz
[Keyworded 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 caseinsensitive. 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 2character
parameter labels are:
A*, B*, C* cell edges
AA, BA, GA cell angles
WL wavelength
ZM, ZD mean and difference of epsilonz
YM, YD mean and difference of epsilony
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 illadvised (probably) to refine beam
parameters other than ET or DH+DV.
DELAY label delay ....
This card takes a series of pairs of parameterlabel, '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 filterlevel 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 nonfractional 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
nonfractional. (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 missetting 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 [ batchspecification ]
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] batchspecification
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, missetting
angles and rocking curve parameters are refined independently for
each film. The keyword ONEMISSET causes the same set of
missetting 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
endoffile 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 multirecord
MTZ file (See section PROGRAM FUNCTION for details)
Output Files
HKLOUT The output reflection data file. This is a multirecord
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(IcorrIref)
= 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(PobsPcal)**2/n]
Q = S/NR = mean delta(fraction)**2/variance
= 1/n Sum[(PobsPcal)**2 / Var(Pobs)]
For all statistics, Pcal = 1 for a fully recorded reflection,
= 0 for a nonrecorded 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 postrefinement 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 phiz, phiy, phix (optionally
different at the two ends of the rotation range). Within
each cycle the program refines the missetting angles in
the camera frame epsilonz and epsilony (ZM and YM), and
optionally their difference ZD and YD, then rotates the
epsilon shifts into the reference frame (phiz, phiy,
phix ) 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 missetting 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 halfwidth of the reflection, but the rockingcurve
parameters ET, DH & DV refer to the fullwidth 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
missetting angle about the rotation axis phiz (epsilonz) 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 missetting (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 Rnative, 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 STRATP 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} << eofsort
BATCH H K L M/ISYM
eofsort
postref:
postref hklin ${dataset}_prfrs_${cycle}
hklout ${dataset}_savep_${cycle}
summary ${saved}/${dataset}_${cycle}.prfsum << eofprf
Title PFK B.st Tstate crystals T9 & T10 cycle ${cycle}
rock tanh limit 2.3 isotropic
crystal 900 to 944
crystal 1000 to 1042
eofprf
# Resort for Rotavata
#
sortmtz hklin ${dataset}_savep_${cycle}
hklout ${dataset}_prfs_${cycle} << eofs1
H K L M/ISYM BATCH
eofs1
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 <<endagro
@${saved}/${dataset}_${cycle}.scales
intensities profile
process full partial all
frmin 0.7
endagro
#
exit
time
trunc:
truncate hklin ${saved}/${dataset}_merge
hklout ${saved}/${dataset}_F <<EOFtrunc
title BST PFK T9 + T10
wilson
#resolution
nresidue 1280
labout F=FT SIGF=SIGFT
EOFtrunc
time
Example 4:
#!/bin/csh f
#
# Postrefinement
#
#
# First resort data on batch
sortmtz hklin $scr0/cx88_scl1 hklout $scr0/bc93_s << eof1
BATCH H K L M/ISYM
eof1
# now for Postref
postref hklin $scr0/bc93_s hklout $scr0/bc93_p << eof2
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
eof2
#
#
# exit
#
# sort back for Rotavata
sortmtz hklin $scr0/bc93_p hklout $scr0/bc93_post << eof3
H K L M/ISYM BATCH
eof3
