mmCIF File Format

From e958358bd83a97494bb11a09f0a5b6d56478e011 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 5 Sep 2016 15:31:02 +0100 Subject: [PATCH] JAL-1919 revised mmCIF documentation --- help/html/features/mmcif.html | 42 +++++++++++++++++++++++------------------ 1 file changed, 24 insertions(+), 18 deletions(-) diff --git a/help/html/features/mmcif.html b/help/html/features/mmcif.html index 6df0fd4..e67f5cd 100644 --- a/help/html/features/mmcif.html +++ b/help/html/features/mmcif.html @@ -5,24 +5,30 @@ mmCIF File Format - mmCIF File Format -

The mmCIF file format (macromolecular Crystallographic - Information) was developed under the auspices of the International Union of Crystallography (IUCr) to extend the Crystallographic Information - File (CIF) data representation used for describing small molecule - structures and associated diffraction experiments.

- Merits of mmCIF file format -

Large structures (containing >62 chains and/or 99999 ATOM - records) that cannot be fully represented in the PDB file format are - available in the PDB archive as single PDBx/mmCIF files.
PDBx/mmCIF file format provides richer data annotation
PDBx/mmCIF became the standard PDB archive format in 2014. - Since 2016 the PDB File Format is no longer being modified or - extended to support new content. -

+ What is mmCIF ? +
mmCIF stands for 'macro-molecular Crystallographic Information + File'. This format was developed by the PDB consortium and the + International Union of Crystallography (IUCr), based on + Crystallographic Information File (CIF), a format used for describing + the structures of small molecules.
mmCIF became the recommended format + for the exchange of biomacromolecular structures in 2014. +

+ mmCIF and Jalview
Since Jalview 2.10, mmCIF + is used for structures downloaded from the PDB. This means: +

Jalview can use the mmCIF to read structures that are too + large to be represented by a single PDB file. (ie, with more than + >62 chains and/or 99999 ATOM records).
Jalview users will have access to the richer annotation + provided by PDBx/mmCIF files.
There may be slight differences between sequences + containing modified residues for structuresÂ downloaded in mmCIF + format. This is because mmCIF differs from the PDB format in the + way it describes non-standard sequence data.

- mmCIF file format support for importing 3D structure data from - flat file and EMBL-PDBe via mmCIF was added in Jalview 2.9.1 + Support for importing 3D structure data from flat file and + EMBL-PDBe as mmCIF was added in Jalview 2.10 \ No newline at end of file -- 1.7.10.2