CIF format, CIFTAB and ShredCIF
CIF format is designed for the archiving, validation and publication of crystallographic data. The ACTA instruction tells SHELXL to write two CIF-format files: name.fcf contains the reflection data and name.cif all other information. In general these files are based on CoreCIF version 2.4.3, with a couple of extensions (e.g. for defining Friedel completeness) which it is hoped will become standard, and several SHELX-specific identifiers that begin with 'shelx'. In general SHELXL tries to put only the information that it knows must be correct into the CIF files, other items are given the value '?'. To maximize the information that it can use, the reflection data should not be merged before running SHELXL. Details of the hardware used and other items that SHELXL cannot know for certain (like the color of the crystal) can be added using programs such as CIFTAB, XCIF, PublCIF or EnCIFer that can combine the CIF file from SHELXL with other CIF files, and in the case of the PublCIF and EnCIFer, also edit the resulting CIF file. Important recent changes in the CIFs generated by SHELXL are discussed here.
It is important to realise that the small molecule CoreCIF is
incompatible with MMCIF, a CIF format used internally by the PDB and by
some macromolecular programs; even the unit-cell demensions have different
names! Since many items in the dialect of CIF used by SHELX-97 have in the
meantime been 'deprecated' and replaced by new CIF identifiers, most
programs that were designed to work with CIF files from SHELXL-97 no longer
work with the current SHELXL, though for important programs such as CheckCIF,
PLATON and Coot this will just be a question of installing an up-to-date
release. It has to be said that the august IUCr COMCIFS committee had no
idea of the amount of chaos it would cause when they replaced
SHELXL now embeds the .res and .hkl files into the output .cif file. This provides a particularly efficient way of archiving a structure determination. The program ShredCIF may be started with:
in order to shred the file name.cif. The output consists of the file name.res renamed as name.ins and the file name.hkl, plus a file name_x.cif that contains the remainder of the shredded CIF file. ShredCIF also checks the checksums of the embedded files to verify that there were no transmission errors. The .ins and .hkl files may be used immediately for a refinement with SHELXL.
CIFTAB reads CIF files and converts them into tables. Bruker users may prefer to rename CIFTAB to XCIF and the template files ciftab.* to xcif.*. The tables produced by CIFTAB/XCIF may prove useful for padding out Ph.D. theses. These programs can also be used to add site-specific CIF items etc. stored in a separate CIF-format file to a CIF file written by SHELXL. CIFTAB is started by the command:
to read the file name.cif. In order to make tables of crystal data, atom parameters, bond lengths and angles, anisotropic displacement parameters and hydrogen atom coordinates, CIFTAB reads a template file that defines how tables should be formatted. Users are encouraged to modify these templates for their own purposes. A 'plain text' template ciftab.def is provided, together with two template files [ciftab.rta (Å) and ciftab.rtm (pm)] for making Rich Text Format (RTF) tables that can be read and edited with most word processors. These templates have not changed since earlier versions of SHELXL, the new CIFTAB (and XCIF) can read both old and new CIF files (but of course the old CIFTAB cannot read the new CIF files). Note that if you wish to use template files that you had prepared yourself for use with the older CIF files, you may need to edit them to update any deprecated CIF names that they use!
This information is provided for those who are interested in modifying the template files provided to add a personal touch to their tables, other CIFTAB users may skip this section. The template file is simply copied to the output file, except that directives (lines beginning with '?' or '$') have special meanings:
A line beginning with
The remaining directives may appear at any point in the format file except immediately after a continuation line marker, but always on a line beginning with '$'.
The hydrogen atom directives apply only to tables of coordinates;
hydrogen atoms are recognized by the ..
The default settings are
The process of converting a virgin SHELXL .cif file into an electronic manuscript for Acta Cryst. Section C may seem at first rather complex and daunting, but fortunately the IUCr provides extensive documentation on using CIF, and a program PublCIF to automate the procedure. Prior to writing up the structure, it is strongly recommended that a CIF file be submitted to the CheckCIF server!