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cifin: interconvert reflection file formats

convert the output of the integration program to a format that structure solution packages (maXus, system S) understand.

Usage

From the unix command line, preferably in the directory where all files of your project reside, type the command:

cifin [options] [inputfilename] [outputfilename]

Both file name arguments are optional. Input files have extensions ".y" (evalccd) or ".sca" (scalepack); output files ".cif" (maXus) or ".hkl" (shelx, system S), Unless both an input and an output file are specified, a window will pop up where you can specify the input and output file names:

If no file names were specified on the command line, the defaults are:

The most recent ".sca" file in the current directory as input file, or, if none exists, "final.y" from any subdirectory.
"import.cif" as output file, or any other file name named as "cifinoutput" in the configuration file

If these defaults are not what you want, you can give alternative filenames on the command line.

Options

The following options are accepted by cifin:

read=filename: Read reflections from the file "filename". Normally this can be acchieved by just naming the filename by itself as argument.
write=filename: Write reflections to the file "filename". Normally this can be acchieved by just naming the filename by itself as argument, except when you want to write a ".hkl" file, it already exists, and you specify it before the input file (in such a case the HKL file is falsely recognized as input file).
gui or nogui: Specifies whether the programs runs in GUI mode (questions will be popped up as windows) or in command line mode (no questions are asked, except if it is necessary to establish the absolute configuration). Default is gui
spacegroup=xxx: specify the space group
formula=xxx: specify the chemical formula (e.g. formula="C4 H9 O6 N" for AMBI)
compound=xxx: Specify the common name for the compound.

Absolute configuration

If the input dataset contains Friedel paired data and you are reading a ".sca" file, the "cifin" program will now try to find out whether your Denzo calibration file is correct or inverse. The 1998 release of denzo inverts the chirality of the data, the 2000 release with correct calibration file gives the correct chirality. At any time, the "cifin" program is able to check the chirality of the dataset and to re-invert it if it appears to be wrong.

For this procedure the program reads a ".x" file from the current directory. If the determination succeeds, a window suggesting the solution will pop up. If the determination fails, cifin will ask you whether your data needs to be inverted. In "nogui" mode, the question will pop up on the command line!

More information for a CIF file

In case the output file is requested in CIF format, a final window will pop up, asking you to specify additional information. Most of the fields will have defaults originating from other DENZO files if they are available in the current directory, or from the command line. Pay special care to fill in the chemical formula field, as it is essential for proper processing by maXus.

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