Information about the Proposed mmCIF-like
Coordinate Format
The CIF Project was
started by the International Union of Crystallography to look into a new
standard format for crystallographic data. CIF (Crystallographic Information
File) is now in general use in the small molecule field. mmCIF is a subset of
this project which is responsible for designing a format for use with
macromolecules.
CCP4 has decided to adopt some of the features of the mmCIF format in its
own working format for co-ordinates. As it is only a working format then only
a subset of the data items described in the mmCIF dictionary will be used.
It is also likely that we would want to expand the mmCIF dictionary to include
additional data items. The format must be editable and easy to read by users
which may put further restrictions on the length of data items. It also
implies that the relationships between the data items should be kept to a
minimum.
Development of the new format is still in its early stages. Following
a meeting on 19/8/97, Martyn Winn (DL) and Liz Potterton (York)
have been coerced into formulating specific proposals. Some ideas
of their thought processes may be got from the following links, but
remember that it is all very fluid at the moment. Feedback welcomed.
Work at Daresbury
- Issues that need to be addressed.
- Documentation for the library routines currently
being developed for working with CIF files.
- A list of programs that have been converted.
- The standard toxd
example coordinate file, represented in CIF. This should be typical of what
a working CIF file will look like, though details may vary. The item labels
are supposed to be self-explanatory, and in particular the layout of
coordinate data should not look too dissimilar to the current restricted PDB file.
-
Ideas from DL.
- An Emacs lisp file which gives a CIF major
mode in Emacs. When loaded (e.g. via .emacs file) this sets the
mode for editing CIF files (not that you should be doing that!).
I find the colour coding very useful, but
you can do more. This will be expanded as I find the time; feedback
welcome! (Previous version available here.)
Work at York
Other resources