mmCIF FORMAT: (CCP4: Formats)
NAME
mmCIF format for CCP4
- the mmCIF format as used in CCP4
The macromolecular Crystallographic Information File (mmCIF) format
was developed by a working group of the IUCr formed in 1990. It
represents an extension of the CIF format used by small molecule
crystallographers, and which is used for automatic submission to Acta
Crystallographica C. mmCIF files are text files with a flexible format
based around either <data_name> <data_value> pairs or a
loop structure (works like a table). In particular, a wide variety of
data items are supported (as defined in the mmCIF dictionary), and
character data values may be lengthy and descriptive. This alleviates
many of the restrictions of the traditional PDB format.
Full details of the mmCIF format can be found on the
mmCIF Home Page or one of its mirrors. Central to the format is the
dictionary of allowed data items. This is designed to be extensible, and
information on proposed extensions is available
here. An mmCIF dictionary is distributed with the CCP4 suite as
$CCP4/lib/data/cif_mm.dic, consisting
of the standard mmCIF dictionary together with some additional data items
required for data harvesting. Note that data
items are grouped into categories.
The mmCIF format is currently used in the CCP4 Suite in the following ways:
- Data Harvesting:
A limited number of programs write out data harvesting files into
a subdirectory of HARVESTHOME (which defaults to the home directory) for
subsequent transfer to deposition sites at the time of structure deposition.
These files are in mmCIF format.
- Reflection files in mmCIF format can
be created the program MTZ2VARIOUS.
- Version 2.7 of RASMOL will read and
display coordinate files in mmCIF format.
- An emacs lisp file for a CIF major mode is distributed as
$CCP4/include/cif.el.
Future uses of mmCIF include:
- The next major version of the refinement program REFMAC will store
restraint information and other intermediate files in mmCIF format.
- It is hoped ultimately to replace
the PDB format by mmCIF as the working coordinate format for the whole
suite, see below.
CCIF coordinate format (not yet implemented)
It is planned to replace the PDB format by mmCIF as the working coordinate
format for the whole suite. Rather than use the full mmCIF format, however,
programs will work with a subset of data items, and additional rules will
be applied. Input and output files may contain additional data items to
the restricted set, but these will simply be copied from input to output.
This restricted format is usually referred to as "CCIF", and is outlined
below.
A set of library routines is distributed which
perform a similar function to the rwbrook
routines. These in turn use Peter Keller's
library of C routines. None of the distributed programs as yet
use these routines, but a set of
sample
programs are available for those that want to try them.
Categories included
The following categories cover the information typically held
in CCP4-PDB files:
- CELL
- cell dimensions (replacing CRYST1 card).
- SYMMETRY
- spacegroup name or number (not normally included in CCP4-PDB files).
- ATOM_SITES
- cell transformations (replacing SCALEx cards).
- ATOM_SITE
- atom site information (replacing ATOM,HETATM,ANISOU cards).
Note:
- ATOM_SITES_ALT, ATOM_SITES_ALT_ENS, ATOM_SITES_ALT_GEN
- pointed to by _atom_site.label_alt_id and gives more information
on alternative conformations: _atom_site.label_alt_id is sufficient
for programs in their current form.
- ATOM_SITE_ANISOTROP
- this contains alternate_exclusive data items to those in
category ATOM_SITE: in general, it is simpler to use the latter.
However, when there is anisotropic U data for only a small subset
of atoms, e.g. for metal ions only, then it might be more convenient
to use a separate category.
In addition, the following categories will also be used:
- AUDIT
- information on how the file was created and subsequently modified.
- ENTITY
- define polymer/non-polymer/water entities.
- ENTITY_POLY_SEQ
- sequence information. Ideally, this should correspond to the
sequence in the ATOM_SITE category, although there are exceptions,
e.g. if the latter describes a temporary poly-ALA model.
- STRUCT_ASYM
- describes contents of asymmetric unit.
- STRUCT_CONN
- describes disulphides, salt bridges and hydrogen bonds. The first
would be useful for protin.
-
-