DTREK2MTZ (CCP4: Supported Program)

NAME

dtrek2mtz - converts d*trek scalemerge output into MTZ format.

SYNOPSIS

dtrek2mtz HKLIN foo.dat HKLOUT foo.mtz
[Keyworded input]

DESCRIPTION

This program converts merged data from d*trek into an MTZ format. After the conversion use TRUNCATE to convert the Is into Fs. Finally, CAD (or sortmtz) should be run to sort the data and put it into the correct asymmetric unit for CCP4.

Assumption: if I+ and I- are on separate lines, then I- appears first. This assumption is checked and a count of the failure of the assumption is output AND I+/I- are swapped. BUT if this happens, you should be very wary of the result mtz file since d*TREK designates I+ and I- properly.

These are converted to the weighted means Imean and SigImean

  Imean = (I+/SIGI+  +  I-/SIGI-) / (1/SIGI+  +  1/SIGI-)
  SigImean = 1 / (1/SIGI+  +  1/SIGI-)

MTZ datasets and Data Harvesting

Columns in MTZ files are organised into projects, crystals and datasets. This information is used in subsequent processing to make sensible decisions based on which dataset a column belongs to. Project, crystal and dataset names should be assigned using the NAME keyword. These will be written to the output MTZ file, and be inherited by subsequent programs. Data harvesting also uses the project and dataset names to write out appropriate harvest files for deposition.

INPUT/OUTPUT FILES

HKLIN

is the input ASCII reflection list file from d*trek. The d*TREK reflection list file usually starts like this:

    nNumIntCols nNumFloatCols nNumStringCols
    column_names
    ...
    4   0   3 51178.9  2796.6

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, END, MONITOR, NAME, REJECT, RESOLUTION, SCALE, SYMMETRY, TITLE
, WAVE

NAME PROJECT <pname> CRYSTAL <xname> DATASET <dname>

[Note that the keywords PNAME <pname>, XNAME <xname> and DNAME <dname> are also available, but the NAME keyword is preferred.]

Specify the project, crystal and dataset names for the output MTZ file. It is strongly recommended that this information is given. Otherwise, the default project, crystal and dataset names are "unknown", "unknown" and "unknown<ddmmyy>" respectively (where <ddmmyy> is the date, with no spaces).

The project-name specifies a particular structure solution project, the crystal name specifies a physical crystal contributing to that project, and the dataset-name specifies a particular dataset obtained from that crystal. All three should be given.

CELL <a> <b> <c> [ <alpha> <beta> <gamma> ]

The cell dimensions in Angstroms and degrees.

If the d*trek reflection list file does not include the cell dimensions, then this keyword is compulsory. The angles default to 90 degrees.

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)/lambdaSquared 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>

If the d*trek reflection list file does not include the spacegroup, then 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.

AUTHOR

J. W. Pflugrath (Dec. 1999) Modified from SCALEPACK2MTZ