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12 Tutorials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

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enCIFer User Guide

1 CIF - The Crystallographic Information File (see page 2)

2 General Features of enCIFer (see page 7)

3 File Operations (see page 13)

4 Text Editor (see page 19)

5 Browser (see page 26)

6 Syntax and Dictionary Checking (see page 29)

7 Loop Editor (see page 45)

8 Data Wizards (see page 51)

9 IUCr CheckCIF/PLATON (see page 57)

10 Visualiser (see page 58)

11 Appendices (see page 72)

12 Tutorials (see page 74)

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enCIFer User Guide

1 CIF - The Crystallographic Information File

1.1 Introduction to the CIF (see page 2)

1.2 Data Names, Data Values and Data Blocks in a CIF (see page 2)

1.3 Looped Lists of Data Items in a CIF (see page 3)

1.4 The CIF Dictionary (see page 4)

1.5 Generating and Editing a CIF (see page 4)

1.6 Depositing CIFs with Journals and the CCDC (see page 5)

1.1 Introduction to the CIF

The small-molecule Crystallographic Information File (CIF: Hall, Allen & Brown, Acta

Crystallographica, A47, 655-685, 1991) is a universal format for the electronic storage and exchange

of crystallographic information. It has been adopted as the international standard for this purpose by

the International Union of Crystallography (IUCr), and is used in:

• Assembling laboratory archives

• Transferring crystallographic information between laboratories

• Depositing crystallographic information with most major journals

• Depositing data with the crystallographic databases

• As a database output format, e.g. for entries retrieved from the Cambridge Structural Database

A CIF is an electronic ASCII file, which is intended to be human readable and editable. It consists of

a set of data items which may appear individually or in looped lists. The lines in a CIF must not

exceed 2048 characters in length, although a soft limit of around 80 characters per line is often used

for easy readability and to ensure facile transmission via e-mail.

Full details of the small-molecule CIF, including leading references, can be found on the IUCr

website at http://www.iucr.org/, and only a brief general introduction is provided here.

1.2 Data Names, Data Values and Data Blocks in a CIF

Every data item is represented by a unique data name followed by its associated data value.

Data items:

• are described in a dictionary which defines meaning and usage

• must start with an underscore (underline) character

• can be any type of string (text, numeric or mixed), ranging from a single character to many lines

of text

Data values are delimited by:

• spaces

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enCIFer User Guide

• double or single quotes, to delimit a data value that contains spaces but does not span lines

• pairs of lines beginning with a semicolon, which delimit multi-line data items

Data values may be set to:

•

(unknown) or

•

(inapplicable).

Related data items, e.g. those which relate to an individual crystal structure are grouped together in a

data block:

• The beginning of a block is designated by the string ‘

data_

’ prefixing the name of the block.

• The end of a block is recognised by another ‘

data_

’ record, or by an end-of-file mark.

These principles are illustrated in the following examples:

data_structure_1

_cell_length_a

5.959(1)

_chemical_formula_moiety

‘C23 H36 O7’

_publ_contact_author

;

Dr S. Motherwell

CCDC

12 Union Road

Cambridge CB2 1EZ

England

;

1.3 Looped Lists of Data Items in a CIF

If a data name is preceded by

loop_

then a series of data values may be associated with it. The

following example shows four data values, individual symmetry operators, associated with a single

data name:

loop_

_symmetry_equiv_pos_as_xyz

‘x, y, z’

‘-x, y+1/2, -z+1/2’

‘-x, -y, -z’

‘x, -y-1/2, z-1/2’

It is also possible to group a series of data values together under a series of different data names, i.e.

to express a table of data values within the CIF, by use of the

loop_

construction. This is illustrated

below for the atom labels and x,y,z-coordinates for four atoms, where the data names can be regarded

as the column headings for a conventional printed table.

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enCIFer User Guide

oop_

_atom_site_label

_atom_site_fract_x

_atom_site_fract_y

_atom_site_fract_z

I1 0.26639(7) 0.61557(3) 0.94292(3)

I2 0.64548(7) 0.36488(3) 0.56299(3)

P3 0.0438(2) 0.27607(11) 0.74432(13)

O1 -0.0989(7) 0.2488(3) 0.6619(4)

The end of a loop is recognised by:

• any new data name, beginning with an underscore

• another

loop_

statement

• a new block starting with a

data_

statement

• an end-of-file mark

1.4 The CIF Dictionary

Valid CIF data names and the permitted data value type(s) for each name are expressed in computer-

readable dictionaries, where the dictionary syntax is define in a separate Dictionary Definition

Language (DDL). Thus, the dictionary entry for

_cell_length_a

specifies that the data value

will be in Angstroms and that a standard uncertainty (ESD) is allowed, placed in parentheses

immediately following the value.

enCIFer is able to load dictionaries which conform to the DLL1.4.1 format (referred to as DDL1)

including the small molecule core dictionary and the powder diffraction dictionary. The current

DDL1 dictionaries available from the IUCr are included in the enCIFer distribution with the

permission of the IUCr, who hold the copyright. EnCIFer supports neither DDL2 nor the proposed

DDLm, CIF files or dictionaries, e.g. the macromolecular CIF dictionary mmCIF.

The latest small-molecule core and other DDL1 dictionaries and details of the DDL can be found on

the IUCr website: http://www.iucr.org/. This site also describes the operation of COMCIFS, the IUCr

Committee that oversees CIF development and the approval of additional CIF data names.

1.5 Generating and Editing a CIF

The crystallographic part of a CIF is normally generated automatically by the software package used

for structure refinement. These CIF generators have been tried and tested over the past decade, and it

is seldom necessary to amend any of these data items. Obviously, the software package can only

output data items that it knows about, i.e. those items that are input to, or are generated by, the

refinement process, or which can reliably be deduced from these data.

enCIFer User Guide

For most purposes, it is necessary to edit into the CIF those additional data items that are needed for

archival purposes, or for transmission of the CIF to a colleague, journal or database. These data items

might include authors’ names and addresses, chemical or physical data, such as chemical compound

names, the melting point, etc.

Some journals permit the text of the manuscript to be incorporated into the CIF using specific data

names. The CIF standard includes support for simple typesetting features such as subscripts,

superscripts and cosequences of multiple ASCII characters (digraphs or trigraphs) to express non-

Roman characters, mathematical symbols etc.

If a CIF is amended or enhanced by manual editing, it is quite easy to destroy the integrity of the CIF

format, so that it cannot be parsed and interpreted by the many programs (structure validation

software, structure visualisers, etc.) that are now designed to read CIF data. It is because of these

pitfalls in manual editing that the enCIFer program has been written.

1.6 Depositing CIFs with Journals and the CCDC

Nearly all journals now expect or require that crystal structure data associated with published papers

shall be deposited in CIF format. Authors should consult the Notes for Authors for their chosen

journal to see their most recent arrangements for depositing CIF data.

Many major journals have arrangements with the Cambridge Crystallographic Data Centre, whereby

the CIF is deposited with the CCDC before the paper is submitted for publication. The CCDC

supplies a CCDC Deposition Number and authors include this number in their submitted manuscript.

This number is printed in the published paper and is stored in the Cambridge Structural Database,

where it affords a valuable link to electronic versions of the journal, and allows scientists to request

individual datasets free of charge from the CCDC.

The CCDC also accepts Private Communications to the CSD, i.e. crystal structures for which formal

journal publication is not envisaged. The data will be checked and evaluated before inclusion in the

CSD, and any problems clarified with the depositor. The author(s) name(s) and contact address will

be included in the CSD.

Full details about CIF deposition to the CCDC, for both journal publications and for private

communications, can be found on the CCDC website at www.ccdc.cam.ac.uk.

enCIFer User Guide

2 General Features of enCIFer

2.1 Acknowledgements (see page 7)

2.2 Scope of the program (see page 7)

2.3 Overview of the Interface (see page 9)

2.4 Command Line Options (see page 10)

2.1 Acknowledgements

The CCDC gratefully

acknowledges the following copyright works, which are used under licence in

EnCIFer:

• Qt, the platform-independent GUI application framework from Trolltech

http://www.trolltech.com

• Mesa C 1999-2001 Brian Paul

http://www.mesa3d.org/

• PCRE library package, by Philip Hazel, and copyright by the University of Cambridge, England

http://www.pcre.org

2.2 Scope of the program

The enCIFer program operates on single or multi-block CIFs to permit:

• Location and reporting of syntax/format violations using the currently enabled dictionary.

• Correction of these syntax/format violations.

• Editing of existing individual data items or looped data items.

• Addition of new individual data items or looped data items.

• Addition of certain standard additional information via two data entry wizards:

• Publication wizard - basic bibliographic information required by most journals and databases

that accept CIF deposition documents.

• Data wizard - chemical and physical property information that enhances a CIF for journal or

database deposition

• Visualisation of structure(s) in the CIF.

• Consistency checks on a small number of data fields

• Additional crystallographic and publication checks via a link to the checkCIF/PLATON service

provided by the IUCr

In all cases where data is edited or added, enCIFer will check the format integrity of the amended file.

Thus, enCIFer is designed to ensure that CIFs are syntactically correct before they are archived,

transmitted or used as input to other software, e.g. data validation programs or structure visualisers.

The visualisation and other checking features also aid users in validating the content and semantics of

enCIFer User Guide

the CIFs.

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