From 4c445258ef7cb8685c6d0b4cf38ec35c3c5cf30c Mon Sep 17 00:00:00 2001
From: tcofoegbu
Date: Thu, 26 May 2016 13:02:43 +0100
Subject: [PATCH] JAL-1919 JAL-1479 user help docs
---
help/html/features/mmcif.html | 28 +++++++++++++++++
help/html/features/seqmappings.html | 2 ++
help/html/features/sifts_mapping_output.png | Bin 0 -> 58182 bytes
help/html/features/siftsmapping.html | 45 +++++++++++++++++++++++++++
help/html/features/viewingpdbs.html | 13 ++++++++
5 files changed, 88 insertions(+)
create mode 100644 help/html/features/mmcif.html
create mode 100644 help/html/features/sifts_mapping_output.png
create mode 100644 help/html/features/siftsmapping.html
diff --git a/help/html/features/mmcif.html b/help/html/features/mmcif.html
new file mode 100644
index 0000000..6df0fd4
--- /dev/null
+++ b/help/html/features/mmcif.html
@@ -0,0 +1,28 @@
+
+
+
+
+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.
+
+
+
+ mmCIF file format support for importing 3D structure data from
+ flat file and EMBL-PDBe via mmCIF was added in Jalview 2.9.1
+
+
\ No newline at end of file
diff --git a/help/html/features/seqmappings.html b/help/html/features/seqmappings.html
index ac63c9e..60ac6ab 100644
--- a/help/html/features/seqmappings.html
+++ b/help/html/features/seqmappings.html
@@ -42,5 +42,7 @@
retrieved by the Sequence Fetcher, and
allows sequence features to be mapped directly from Uniprot das
sources to their coding region on EMBL sequence records.
+
+ In Jalview 2.9.1 SIFTS Mapping was added as a better means for explicitly identifying the coordinates corresponding to a displayed sequence when viewing a PDB structure associated with a sequence