SCALEPACK2MTZ (CCP4: Supported Program)
NAME
scalepack2mtz
- converts merged scalepack output into MTZ format.
SYNOPSIS
scalepack2mtz
HKLIN
foo.dat
HKLOUT
foo.mtz
[Keyworded input]
DESCRIPTION
This program converts merged data from scalepack (which is part of the
DENZO package) into an MTZ format. The scalepack data file may or may not
contain anomalous data. After the conversion use
TRUNCATE to convert the Is into Fs.
Finally, CAD should be run to sort the data and put it
into the correct asymmetric unit for CCP4.
Data Harvesting
Data harvesting (and some other functionality)
relies on the existence of appropriate project and dataset names, and these
should be assigned in SCALEPACK2MTZ using the PNAME and
DNAME keywords. These will be written to the the
output MTZ file, and be inherited by subsequent programs.
INPUT/OUTPUT FILES
- HKLIN
-
is the input ASCII scalepack file. It is assumed to start with a 3-line
header, the third line containing the cell dimensions. In the absence of
anomalous data there should be 5 columns H, K, L, I and SIGI, and with
anomalous data there should be 7 columns H, K, L, I+, SIGI+, I- and SIGI-.
- HKLOUT
-
is the output MTZ file containing labels H, K, L, IMEAN, SIGIMEAN and if
anomalous data is present I(+), SIGI(+), I(-), SIGI(-) as well.
KEYWORDED INPUT
Available keywords are:
ANOMALOUS, CELL,
DNAME, END,
MONITOR, PNAME,
REJECT, RESOLUTION,
SCALE, SYMMETRY,
TITLE, WAVE
The only compulsory keyword is SYMMETRY.
PNAME <projectname>
[default: 'unknown']
Project Name used for Data Harvesting.
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 <datasetname>
[default: 'unknown<ddmmyy>']
Dataset Name used for Data Harvesting.
This keyword is not compulsory, but is
advisable to obtain a sensible name rather than 'unknown<ddmmyy>'
(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.
CELL <a> <b> <c> [ <alpha> <beta> <gamma> ]
The cell dimensions in Angstroms and degrees.
The angles default to 90 degrees. If this key
is omitted then the cell dimensions are taken
from the input file (normally OMIT this command).
ANOMALOUS YES | NO
Specify whether or not input file contains anomalous data.
Defaults to YES.
MONITOR <nmon>
Monitors the <nmon>th reflection and writes it to the output stream. The
default is every 1000th reflection.
REJECT <h k l>
If specified then the specific hkl will not be written to the MTZ file.
RESOLUTION <maxres> <minres>
If specified then the all reflections outside the range will be excluded from
the MTZ file. The limits can be given in either order and in Angstrom or
SineSquared(theta)/LamdaSquared units. The default is that all reflections
are output.
SCALE <scale>
All intensities and their sigmas will be scaled by <scale>. The default is
1.0.
SYMMETRY <SG name|SG number>
This keyword is compulsory and can be given as the space group name or
number.
TITLE <string>
This title will become the title/history in the MTZ file.
WAVE <wavelength>
The wavelength associated with this data. (Will become compulsory)
END
Terminates the keyword input. Must be last keyword.
EXAMPLES
A unix example scipt is availabe in $CEXAM/unix/runnable/
scalepack2mtz.exam
SEE ALSO
cad,
truncate,
Data Harvesting.