From: Jim Procter
Date: Thu, 26 May 2016 14:21:24 +0000 (+0100)
Subject: Merge branch 'develop' of http://source.jalview.org/git/jalview into develop
X-Git-Tag: Release_2_10_0~212^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e00d0cbf84f4a2a21a927e9c017c3a69fc436704;hp=a66ef4094d32ee13d64bb63139fe3cb33c3a04dc;p=jalview.git
Merge branch 'develop' of source.jalview.org/git/jalview into develop
---
diff --git a/examples/exampleFeatures.txt b/examples/exampleFeatures.txt
index 2dc4b6d..c0098a9 100755
--- a/examples/exampleFeatures.txt
+++ b/examples/exampleFeatures.txt
@@ -26,73 +26,74 @@ BETA-TURN-IIL 8b5b50
ST-MOTIF ac25a1
STARTGROUP uniprot
+Pfam family FER_CAPAA -1 0 0 Pfam
Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL
Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL
Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL
Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL
-Fer2 Status: True Positive Pfam 8_8 FER_CAPAA -1 8 83 Pfam
+Fer2 Status: True Positive Pfam 8_8 FER_CAPAA -1 8 83 Pfam
Ferredoxin_fold Status: True Positive FER_CAPAA -1 3 93 Cath
Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL
-Fer2 Status: True Positive Pfam 55_13 FER_CAPAN -1 55 130 Pfam
+Fer2 Status: True Positive Pfam 55_13 FER_CAPAN -1 55 130 Pfam
Ferredoxin_fold Status: True Positive FER_CAPAN -1 45 140 Cath
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL
-Fer2 Status: True Positive Pfam 55_13 FER1_SOLLC -1 55 130 Pfam
+Fer2 Status: True Positive Pfam 55_13 FER1_SOLLC -1 55 130 Pfam
Ferredoxin_fold Status: True Positive FER1_SOLLC -1 45 140 Cath
-Fer2 Status: True Positive Pfam 55_13 Q93XJ9_SOLTU -1 55 130 Pfam
+Fer2 Status: True Positive Pfam 55_13 Q93XJ9_SOLTU -1 55 130 Pfam
Ferredoxin_fold Status: True Positive Q93XJ9_SOLTU -1 45 140 Cath
Iron-sulfur (2Fe-2S) FER1_PEA -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER1_PEA -1 96 96 METAL
Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL
Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL
-Fer2 Status: True Positive Pfam 60_13 FER1_PEA -1 60 135 Pfam
+Fer2 Status: True Positive Pfam 60_13 FER1_PEA -1 60 135 Pfam
Ferredoxin_fold Status: True Positive FER1_PEA -1 50 145 Cath
-Fer2 Status: True Positive Pfam 63_13 Q7XA98_TRIPR -1 63 138 Pfam
+Fer2 Status: True Positive Pfam 63_13 Q7XA98_TRIPR -1 63 138 Pfam
Ferredoxin_fold Status: True Positive Q7XA98_TRIPR -1 53 148 Cath
Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL
-Fer2 Status: True Positive Pfam 59_13 FER1_MESCR -1 59 134 Pfam
+Fer2 Status: True Positive Pfam 59_13 FER1_MESCR -1 59 134 Pfam
Ferredoxin_fold Status: True Positive FER1_MESCR -1 49 144 Cath
Iron-sulfur (2Fe-2S) FER1_SPIOL -1 89 89 METAL
Iron-sulfur (2Fe-2S) FER1_SPIOL -1 94 94 METAL
Iron-sulfur (2Fe-2S) FER1_SPIOL -1 97 97 METAL
Iron-sulfur (2Fe-2S) FER1_SPIOL -1 127 127 METAL
-Fer2 Status: True Positive Pfam 58_13 FER1_SPIOL -1 58 133 Pfam
+Fer2 Status: True Positive Pfam 58_13 FER1_SPIOL -1 58 133 Pfam
Ferredoxin_fold Status: True Positive FER1_SPIOL -1 48 143 Cath
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 47 47 METAL
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL
-Fer2 Status: True Positive Pfam 8_8 FER3_RAPSA -1 8 83 Pfam
+Fer2 Status: True Positive Pfam 8_8 FER3_RAPSA -1 8 83 Pfam
Ferredoxin_fold Status: True Positive FER3_RAPSA -1 3 93 Cath
Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL
Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL
Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL
Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL
-Fer2 Status: True Positive Pfam 8_8 FER_BRANA -1 8 83 Pfam
+Fer2 Status: True Positive Pfam 8_8 FER_BRANA -1 8 83 Pfam
Ferredoxin_fold Status: True Positive FER_BRANA -1 2 96 Cath
Iron-sulfur (2Fe-2S) FER2_ARATH -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER2_ARATH -1 96 96 METAL
Iron-sulfur (2Fe-2S) FER2_ARATH -1 99 99 METAL
Iron-sulfur (2Fe-2S) FER2_ARATH -1 129 129 METAL
-Fer2 Status: True Positive Pfam 60_13 FER2_ARATH -1 60 135 Pfam
+Fer2 Status: True Positive Pfam 60_13 FER2_ARATH -1 60 135 Pfam
Ferredoxin_fold Status: True Positive FER2_ARATH -1 50 145 Cath
-Fer2 Status: True Positive Pfam 60_11 Q93Z60_ARATH -1 60 118 Pfam
+Fer2 Status: True Positive Pfam 60_11 Q93Z60_ARATH -1 60 118 Pfam
Ferredoxin_fold Status: True Positive Q93Z60_ARATH -1 52 118 Cath
Iron-sulfur (2Fe-2S) FER1_MAIZE -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER1_MAIZE -1 96 96 METAL
Iron-sulfur (2Fe-2S) FER1_MAIZE -1 99 99 METAL
Iron-sulfur (2Fe-2S) FER1_MAIZE -1 129 129 METAL
-Fer2 Status: True Positive Pfam 60_13 FER1_MAIZE -1 60 135 Pfam
+Fer2 Status: True Positive Pfam 60_13 FER1_MAIZE -1 60 135 Pfam
Ferredoxin_fold Status: True Positive FER1_MAIZE -1 50 145 Cath
-Fer2 Status: True Positive Pfam 52_12 O80429_MAIZE -1 52 127 Pfam
+Fer2 Status: True Positive Pfam 52_12 O80429_MAIZE -1 52 127 Pfam
Ferredoxin_fold Status: True Positive O80429_MAIZE -1 42 137 Cath
ENDGROUP uniprot
diff --git a/examples/plantfdx.features b/examples/plantfdx.features
index a23d152..872dadc 100644
--- a/examples/plantfdx.features
+++ b/examples/plantfdx.features
@@ -14,22 +14,22 @@ Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL
Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL
Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL
Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL
-Description: Fer2 Status: True Positive Pfam 8_83 FER_CAPAA -1 8 83 Pfam
+Description: Fer2 Status: True Positive Pfam 8_83 FER_CAPAA -1 8 83 Pfam
Chloroplast FER_CAPAN -1 1 47 TRANSIT
Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL
Phosphothreonine FER_CAPAN -1 136 136 MOD_RES
-Description: Fer2 Status: True Positive Pfam 55_130 FER_CAPAN -1 55 130 Pfam
+Description: Fer2 Status: True Positive Pfam 55_130 FER_CAPAN -1 55 130 Pfam
Chloroplast FER1_SOLLC -1 1 47 TRANSIT
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL
-Description: Fer2 Status: True Positive Pfam 55_130 FER1_SOLLC -1 55 130 Pfam
+Description: Fer2 Status: True Positive Pfam 55_130 FER1_SOLLC -1 55 130 Pfam
Evidence: EI4 Q93XJ9_SOLTU -1 1 48 SIGNAL
-Description: Fer2 Status: True Positive Pfam 55_130 Q93XJ9_SOLTU -1 55 130 Pfam
+Description: Fer2 Status: True Positive Pfam 55_130 Q93XJ9_SOLTU -1 55 130 Pfam
Chloroplast FER1_PEA -1 1 52 TRANSIT
L -> I (in strain: cv. Onward) FER1_PEA -1 59 59 VARIANT
I -> L (in strain: cv. Onward) FER1_PEA -1 85 85 VARIANT
@@ -38,14 +38,14 @@ Iron-sulfur (2Fe-2S) FER1_PEA -1 96 96 METAL
Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL
Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL
YPTS -> PPPA (in Ref. 2) FER1_PEA -1 132 135 CONFLICT
-Description: Fer2 Status: True Positive Pfam 60_135 FER1_PEA -1 60 135 Pfam
-Description: Fer2 Status: True Positive Pfam 63_138 Q7XA98_TRIPR -1 63 138 Pfam
+Description: Fer2 Status: True Positive Pfam 60_135 FER1_PEA -1 60 135 Pfam
+Description: Fer2 Status: True Positive Pfam 63_138 Q7XA98_TRIPR -1 63 138 Pfam
Chloroplast FER1_MESCR -1 1 51 TRANSIT
Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL
-Description: Fer2 Status: True Positive Pfam 59_134 FER1_MESCR -1 59 134 Pfam
+Description: Fer2 Status: True Positive Pfam 59_134 FER1_MESCR -1 59 134 Pfam
Chloroplast FER1_SPIOL -1 1 50 TRANSIT
STRAND FER1_SPIOL -1 52 59 STRAND
TURN FER1_SPIOL -1 60 61 TURN
@@ -68,7 +68,7 @@ Iron-sulfur (2Fe-2S) FER1_SPIOL -1 127 127 METAL
STRAND FER1_SPIOL -1 130 133 STRAND
STRAND FER1_SPIOL -1 135 138 STRAND
HELIX FER1_SPIOL -1 142 144 HELIX
-Description: Fer2 Status: True Positive Pfam 58_133 FER1_SPIOL -1 58 133 Pfam
+Description: Fer2 Status: True Positive Pfam 58_133 FER1_SPIOL -1 58 133 Pfam
I -> V FER3_RAPSA -1 8 8 VARIANT
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL
@@ -77,25 +77,25 @@ S -> T FER3_RAPSA -1 55 55 VARIANT
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL
R -> K FER3_RAPSA -1 91 91 VARIANT
M -> V FER3_RAPSA -1 95 95 VARIANT
-Description: Fer2 Status: True Positive Pfam 8_83 FER3_RAPSA -1 8 83 Pfam
+Description: Fer2 Status: True Positive Pfam 8_83 FER3_RAPSA -1 8 83 Pfam
Chloroplast FER1_ARATH -1 1 52 TRANSIT
Iron-sulfur (2Fe-2S) FER1_ARATH -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER1_ARATH -1 96 96 METAL
Iron-sulfur (2Fe-2S) FER1_ARATH -1 99 99 METAL
Iron-sulfur (2Fe-2S) FER1_ARATH -1 129 129 METAL
-Description: Fer2 Status: True Positive Pfam 60_135 FER1_ARATH -1 60 135 Pfam
+Description: Fer2 Status: True Positive Pfam 60_135 FER1_ARATH -1 60 135 Pfam
Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL
Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL
Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL
Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL
-Description: Fer2 Status: True Positive Pfam 8_83 FER_BRANA -1 8 83 Pfam
+Description: Fer2 Status: True Positive Pfam 8_83 FER_BRANA -1 8 83 Pfam
Chloroplast FER2_ARATH -1 1 52 TRANSIT
Iron-sulfur (2Fe-2S) FER2_ARATH -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER2_ARATH -1 96 96 METAL
Iron-sulfur (2Fe-2S) FER2_ARATH -1 99 99 METAL
Iron-sulfur (2Fe-2S) FER2_ARATH -1 129 129 METAL
-Description: Fer2 Status: True Positive Pfam 60_135 FER2_ARATH -1 60 135 Pfam
-Description: Fer2 Status: True Positive Pfam 60_118 Q93Z60_ARATH -1 60 118 Pfam
+Description: Fer2 Status: True Positive Pfam 60_135 FER2_ARATH -1 60 135 Pfam
+Description: Fer2 Status: True Positive Pfam 60_118 Q93Z60_ARATH -1 60 118 Pfam
Chloroplast FER1_MAIZE -1 1 52 TRANSIT
STRAND FER1_MAIZE -1 57 59 STRAND
STRAND FER1_MAIZE -1 72 74 STRAND
@@ -113,6 +113,6 @@ Iron-sulfur (2Fe-2S) FER1_MAIZE -1 129 129 METAL
STRAND FER1_MAIZE -1 132 135 STRAND
STRAND FER1_MAIZE -1 137 141 STRAND
TURN FER1_MAIZE -1 142 142 TURN
-Description: Fer2 Status: True Positive Pfam 60_135 FER1_MAIZE -1 60 135 Pfam
-Description: Fer2 Status: True Positive Pfam 52_127 O80429_MAIZE -1 52 127 Pfam
+Description: Fer2 Status: True Positive Pfam 60_135 FER1_MAIZE -1 60 135 Pfam
+Description: Fer2 Status: True Positive Pfam 52_127 O80429_MAIZE -1 52 127 Pfam
ENDGROUP uniprot
diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html
index 9164afd..200fc8f 100755
--- a/help/html/features/featuresettings.html
+++ b/help/html/features/featuresettings.html
@@ -104,7 +104,7 @@
the bottom of the list is rendered below a feature higher
up in the list.
You can change
the order of a feature by dragging it up and down the list with
- the mouse.
+ the mouse (not applet).
The Optimise order button (currently only
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