ROTAPREP (CCP4: Deprecated Program)
NAME
rotaprep
- produces an MTZ file in multirecord form suitable for input to SCALA.
SYNOPSIS
rotaprep hklin foo.mtz hklout foo.mtz
[Keyworded input]
DESCRIPTION
The rotaprep program has been replaced by
COMBAT. Please use this alternative
supported program. Rotaprep will be 'phased out'.
This program converts output from assorted data processing programs into a
multirecord MTZ file suitable for input to the CCP4 scaling and merging
programs (SCALA and TRUNCATE). Only mosflm writes such an MTZ file.
Input types accepted at present are: DATRED_RIGAKU, DENZO,
JIMS, MTZF, MTZI, MUF, MUI, RAXISDUMP, SAINT,
various SCALEPACK options , TEXHKL, TEXSAN, USER,
WEISS, XDSFULL, XDSUNIQUE.
Some of these are quite rare, but it seems sensible to keep them.
It would be trivial to extend the program for any format.
Warning: It is quite likely
that the authors of processing programs will change their formats
without telling CCP4. If you have any queries or knowledge of such changes please contact us.
Data Harvesting
Data harvesting (and some other functionality)
relies on the existence of appropriate project and dataset names, and these
should be assigned in ROTAPREP using the PNAME and
DNAME keywords. These will be written to the
output MTZ file, and be inherited by subsequent programs.
INPUT FORMATS
The following arguments to the INPUT keyword are supported. The most commonly
used arguments are those used to convert existing MTZ files, or options for DENZO
or SCALEPACK outputs (keywords DENZO, SCAL_NM and SCAL_NM2).
These are described first. The items
in the descriptions of the format have the following interpretations:
- h k l
- Miller indices (possibly unique ones);
- F sigF
- Measured structure factor amplitude and its standard deviation;
- I sigI
- Measured intensity and its standard deviation;
- delI sigdelI
- Anomalous intensity difference and its standard deviation;
- ident / ibatch
- Batch number or equivalent;
- mpart / fpart
- Partiality flag (in some convention).
MTZI
Standard MTZ file containing h k l I sigI. It is possible to read in
a standard MTZ format file containing h k l I sigI and produce a `multirecord'
MTZ file. You may wish to use a set of processed data as a
reference `batch' for SCALA.
MTZF
Standard MTZ file containing h k l F sigF. It is possible to read in
a standard MTZ format file containing h k l F sigF and produce a `multirecord'
MTZ file. You may wish to use a set of processed data as a
reference `batch' for SCALA.
DENZO
Concatenated output files from DENZO. These contain HEADER blocks
and reflection data. [h k l fsqp I sigI fpart phi] in format (3I4, 2X, 2F8.0,
7X, F6.0, 6X, 2F7.0, 14X, 2F6.0)
Care is needed when doing this, since no post-refinement has been done.
We now prefer to run SCALEPACK to refine the cell and orientation,
then either run DENZO again to re-integrate the images without re-refining
the cell etc. (however there may still be problems with partiality flags), or
output an unmerged file from scalepack (see keywords SCAL_NM and SCAL_NM2).
- N.B. If using the commercialised Denzo identified like:
HKL data processing system Version 1.0 FT1.31 Rev1.4
you need to use the Denzo command
film york output file <filename>
to produce a suitable format for `rotaprep'. The `york' output can also
be read into `scalepack' with
format denzo_york1
SCAL_NM
Output from SCALEPACK option NOMERGE no partials [h k l ibatch
isym I SigI (Fpart)] in format (4i4,i3,2f8.0,f7.2). Scales have been applied
and partials summed. The Friedel pairs are separate in this case.
SCAL_NM2
Output from SCALEPACK option NOMERGE original indices
[h k l h0 k0 l0 ibatch I SigI] in format (6I4,i6,7x,2f8.0). Scales have been
applied and partials summed. The Friedel pairs are separate in this case.
DATRED_RIGAKU
[h k l F sigF] in format (3i4,4f8.1).
JIMS
MADNES for050 files.
[h k l I sigI] in format (3i5,2f10.2).
MUI
For intensities output from the XENTRONICS and XENGEN
data processing packages.
[format (3i4, 1x, F6.4, 6(1x,f8.2), 1x, i2).]
MUF
For amplitudes output from the XENTRONICS and XENGEN
data processing packages.
[format (3i4, 1x, F6.4, 6(1x,f8.2), 1x, i2).]
RAXISDUMP
Output from Raxis READBF of mergefile.
[mpart h k l I sigI ibatch] in
format (21x, I4, 4x, 3i4, 8x, 2f10.3, i4).
- Note: if you use the `log' file produced under unix rather than the
`output' file you may need to change the format to eat an extra space, i.e.
start it with `22x'. Note also that you may find alternative processing
packages to be better than the Raxis software.
SAINT
Output from SAINT, one batch only (not fully tested).
SCALEPACK
Output from SCALEPACK [h k l I+ SigI+ I- SigI-]
in format (3i4,4f8.0).
N.B.
This is not a very useful option. It is better to run SCALEPACK2MTZ and
TRUNCATE on the
scalepack output, then use the MTZI option with the truncate output.
TEXSAN
Output from TEXSAN data processing package for Rigaku diffractometer.
[h k l ident I sigI] in format (3i4, i3, 5x, f8.1, f7.1).
TEXHKL
Output from TEXSAN data processing package for Rigaku diffractometer.
[h k l I sigI scale] in format (3x, 3i4, 2F10.2, 29x, F7.4).
USER
ASCII data file in a user-defined format, see LABEL and FORMAT keywords.
WEISS
Output from the WEISS data processing package for Japanese Weissenberg
data. [h k l mpart I sigI ident] in format (5x, 4i4, 2f8.2, i10).
XDSUNIQUE
Output from Kabsch's XDS data processing package (or the MAR
Research version) in the standard text file UNIQUE.HKL from the
CORRECT stage. [The output of the MARSCALE program (and possibly
the original XSCALE) can also be put in this form, although there
is probably no reason to prefer these to scala]. This file contains
symmetry averaged reflection intensities and anomalous differences after
scaling.
[h k l I sigI delI sigdelI] in format (3I5, 4E12.4)
Since UNIQUE output is scaled and merged, it is sensible to use `f2mtz'
to produce an MTZ file for direct input to `truncate'.
XDSFULL
Output from Kabsch's XDS data processing package (or the MAR
Research version) in the standard direct access binary file XDS.HKL
from the CORRECT stage. This contains scaled intensities of all reflections
before symmetry averaging. Note that this file type will not be generally
portable between computer systems - run `rotaprep' on the system which
generated xds.hkl.
DESCRIPTION OF THE OUTPUT MTZ FILE
The output file has the column labels:
- H K L
- Miller indices.
- M/ISYM
- 256*M + ISYM, where the partiality flag M=0 for fully recorded reflexions
and M=1 for partials, and ISYM is the symmetry number.
- BATCH
- Batch (serial) number for this film/image.
- I, sigI
- Corrected integrated intensity and its standard deviation.
- FRACTIONCAL
- This is Calculated fraction recorded*1000 (>500 if partial more
than half present). For most inputs FRACTIONCAL is a dummy set to 3000
or 501 for a partial.
- RATDELSD
- 1000*ratio of worst delta(I)/STD.DEVN found within a film pack.
- IPR, sigIPR
- is meant to be corrected profile-fitted intensity and SD. Here IPR
and sigIPR are set equal to I and sigI if there is no appropriate information
input.
- XDET, YDET, ROT
- Detector position and PHI angle. This information is available for
DENZO & SAINT only.
KEYWORDED INPUT
Available keywords are:
ADDBATCH, BATCH,
CELL, DETECTOR,
DNAME, END,
FORMAT, INPUT,
LABEL, LABIN,
MISBATCH, MONITOR,
PHIRANGE, PNAME,
REINDEX, REJECT,
RESOLUTION, SCALE,
SYMMETRY, TITLE
Compulsory input keywords for some options:
INPUT <type>
The allowed <type>s are those listed above.
BATCH <batch number>
This specifies the `batch' number for data in the multirecord MTZ
output. (BATCH is not required for DENZO, SCAL_NM, SCAL_NM2, SAINT or USER input
if a batch column is present in the input file. It is not required for
WEISS or TEXSAN inputs but if given it will override the IDENT value.)
CELL <a> <b> <c> [ <alpha>
<beta> <gamma> ]
Cell dimensions in Angstroems and angles in degrees; the angles default
to 90 degrees. This keyword is not compulsory for MTZF,
MTZI, SCAL_NM or
DENZO input, but if given it will override the
cell dimensions from the file headers. This keyword is compulsory for
other input types.
LABIN <program label> = <file label>
...
Only compulsory for MTZF or MTZI input.
Column assignments for conventional labels F and SIGF are required
for MTZF input, or for I and SIGI for MTZI input.
LABEL <file label 1> <file label 2>
...
Column assignments for user-defined input format (INPUT USER). <file
label n> must be chosen from H, K, L, M, BATCH, I, SIGI (or F, SIGF),
IPR, SIGIPR, FRACTION and given in the order in which they occur in the
input file. The indices H, K, L are compulsory. M is optional and defaults
to 0, i.e. fully recorded reflexions. The batch number should either be
read in from a BATCH column or taken from the BATCH keyword (the former
takes precedence if both are present). Either I, SIGI or F, SIGF must be
given; if the latter, then F is squared and I/SIGI output. The remaining
columns IPR, SIGIPR, FRACTION are optional.
SYMMETRY <SG number> | <SG symbol>
Specifies the spacegroup for the data. Compulsory if not
MTZF or MTZI input.
Optional input keywords:
For input types which contain batch number information the following
three keywords determine the transformation of the input numbers:
ADDBATCH <offset>
<offset> is added to all input batch numbers (default 0).
MISBATCH <batch1> <batch2> ...
For inputs with batch information e.g. DENZO, then the number of batch
headers written to the MTZ file is from the maximum batch value to the
minimum. If some batches are missing, in this range, then use the MISBATCH
keyword to exclude them from the header. This keyword can only be used
once and is not for excluding batches from the data.
PHIRANGE <divisions>
(DENZO only, default 1.) Each batch is split into a number <divisions>
of divisions for scaling.
The output batch number will be:
<divisions>*(batch - 1) + phi_step_counter + <offset>
FORMAT <format string>
Supply a format specifier for user-defined input (see INPUT USER).
The argument must be a valid FORTRAN fixed format string, such as might
be given in a FORMAT statement, including the brackets and quoted. E.g.:
FORMAT '(6(6X,F8.3))'
will read records comprising six numbers each preceded by a six-character-wide
field which will be skipped. It is not possible to read more than one reflexion
from each input line. Make sure the format is reading real numbers
(F), and not integers (I)! If your input file contains integers, read them
with e.g. F6.0 rather than I6. Make use of the X descriptor to skip unwanted
columns. Under Unix, the cut (1) command may be useful for reformatting
the input columns if, for instance, the relevant fields aren't in fixed
positions. If the FORMAT keyword is not given for user-defined input, then
the default format specifier '*' is used.
PNAME <project name>
[default: 'unknown']
This keyword can be used to assign a project name for HKLOUT.
For input options MTZF and MTZI, a project name given by this keyword
overrides any in HKLIN.
This keyword is not compulsory, but is advisable to obtain a sensible name.
A dataset, as listed in the MTZ header, is specified by a project-name/dataset-name
pair. The project-name specifies a particular structure solution project,
while the dataset-name specifies a particular dataset contributing to the
structure solution. An entry in the PNAME keyword should therefore be
accompanied by a corresponding entry in the DNAME keyword.
DNAME <dataset name>
[default: 'unknownddmmyy']
This keyword can be used to assign a dataset name for HKLOUT.
For input options MTZF and MTZI, a dataset name given by this keyword
overrides any in HKLIN.
This keyword is not compulsory, but is advisable to obtain a sensible name rather than
'unknownddmmyy' (where ddmmyy is the date, with no spaces).
A dataset, as listed in the MTZ header, is specified by a project-name/dataset-name
pair. The project-name specifies a particular structure solution project,
while the dataset-name specifies a particular dataset contributing to the
structure solution. An entry in the DNAME keyword should therefore be
accompanied by a corresponding entry in the PNAME keyword.
MONITOR <nmon>
Every <nmon>-th reflection is monitored (printed out). Default:
no monitoring.
REJECT <hrej> <krej> <lrej>
The arguments specify indices of reflections to be excluded from the output
file (these indices should lie in the spacegroup's chosen asymmetric unit).
All reflections equivalent to this set of indices will be rejected. This
is a desperate measure to weed out bad reflections (usually overloads)
without repeating the data processing. This line can be repeated up to
200 times.
REINDEX <transformation>
<transformation> specifies how to transform the original indices
for the output. It is specified in the form k,h,-l; h,-k,-h/2-1/2; etc.
The default is no transformation.
RESOLUTION <resmin> [ <resmax>
]
Rejects reflections outside the given resolution range in Ås or 4s**2/lambda**2.
SCALE <scale>
The input intensities are multiplied by <scale> (default 1.0).
TITLE <title>
<title> is written to the output file.
DETECTOR <xmin> <xmax> <ymin>
<ymax>
limits of detector coordinates XDET, YDET. These are needed for the
detector scaling options in Scala.
END
to finish.
SEE ALSO
scala, f2mtz, Data Harvesting, CAD,
`The marxds marscale manual', MAR Research.
EXAMPLES
rotaprep HKLIN raxis.dump HKLOUT junk.mtz << +
CELL 63 63 264 90 90 90
MONITOR 1000
BATCH 1 # first batch number
INPUT RAXISDUMP
RESOLUTION 0 0.137
SYMMETRY 89
TITLE Test rota_prep
PNAME myproject
DNAME native
END
+
/y/ccp4/cadd/junk/rotaprep \
HKLIN ~rick/ESRF/pcrb/pcrb5_e1.sca \
HKLOUT $SCRATCH/pcrb5_e1.mtz \
<< 'END-mtzrwrot'
MONI 10000
INPUT SCAL_NM2
ADDBATCH 0
CELL 92.004 92.004 175.229 90.000 90.000 90.000
SYMM P41212
TITLE Test on Scalepack - NoMerge- Original Indices L1
PNAME myproject
DNAME native
END
'END-mtzrwrot'
#
AUTHOR
Eleanor Dodson, University of York