From: tcofoegbu Date: Thu, 26 May 2016 12:02:43 +0000 (+0100) Subject: JAL-1919 JAL-1479 user help docs X-Git-Tag: Release_2_10_0~217 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4c445258ef7cb8685c6d0b4cf38ec35c3c5cf30c;p=jalview.git JAL-1919 JAL-1479 user help docs --- 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 + + + 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

diff --git a/help/html/features/sifts_mapping_output.png b/help/html/features/sifts_mapping_output.png new file mode 100644 index 0000000..3c28b81 Binary files /dev/null and b/help/html/features/sifts_mapping_output.png differ diff --git a/help/html/features/siftsmapping.html b/help/html/features/siftsmapping.html new file mode 100644 index 0000000..c344a20 --- /dev/null +++ b/help/html/features/siftsmapping.html @@ -0,0 +1,45 @@ + + + + +SIFTS Mapping + + + +

SIFTS Mapping

+ +

+ SIFTS (Structure integration with function, taxonomy + and sequences) provides an up-to-date resource for residue-level + mapping between Uniprot and PDB entries. The information is updated and + released weekly simultaneously with the release of new PDB entries. + SIFTS Entries are published as XML files and made publicly available via an FTP + site hosted at the European Bioinformatics Institute. +

+ +

+ At the point of viewing a PDB structure, Jalview downloads a SIFTS file + for the target entry and uses it to accurately map the sequence residues with the + structure residue. Prior to SIFTS integration, Jalview uses Needleman and Wunsch + Alignment algorithm to map sequence residues to structure residues, and that may not + always result to a correct mapping since it is computational determined. +

+ +

+ The default method for 'Sequence ↔ Structure' mapping can be configured + in the Structure tab in the Tools → Preferences dialog box. When 'SIFTS' + is enabled as the default, all mappings between 'Sequence ↔ Structure' is + performed via SIFTS provided that there is a valid SIFTS entry for PDB structure. If no + valid SIFTS resource is available, then the 'Sequence ↔ Structure' mapping falls + back to Needleman and Wunsch Alignment algorithm. +

+ +

To verify the mapping method used, you can view the mapping output via the structure viewer menu File → View mapping. A sample mapping output can be seen in the screenshot below. The highlighted position shows the method used.

+

+ SIFTS mapping output +

+ +

SIFTS Mapping integration was added in Jalview 2.9.1

+ + + \ No newline at end of file diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 4d35516..d4819f1 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -121,6 +121,19 @@

+ Importing PDB Entries or files in mmCIF format
+ mmCIF file format provides an alternative means for + importing 3D structure data from flat file and EMBL-PDBe + web-service. To enable mmCIF as the default format for + importing PBD sequences from the PDB sequence fetcher, add or modify the + property + DEFAULT_STRUCTURE_FORMAT=mmCIF in Jalview properties file. + Once this is done, the steps followed in retrieving PDB format files above can + be followed to obtain the same data with mmCIF. mmCIF format file support was added in Jalview 2.9.1.

+ + + +

Associating a large number of PDB files to sequences in an alignment
It is often the case when working with structure alignments that you will have a directory of PDB