Annotation from 3D structure data

From b8eecc11ecdeebc95f00014b5e588a583211ea32 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 18 Nov 2014 09:44:36 +0000 Subject: [PATCH 1/1] JAL-674 JAL-1512 JAL-1333 documentation --- help/html/features/preferences.html | 13 +++-- help/html/features/viewingpdbs.html | 28 +++++++--- help/html/features/xsspannotation.html | 90 ++++++++++++++++++++++++++++++++ 3 files changed, 116 insertions(+), 15 deletions(-) create mode 100644 help/html/features/xsspannotation.html diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index b2d8b93..5d4ab4d 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -113,13 +113,12 @@ will be loaded.

"Structure" Preferences tab added in Jalview 2.8.2

Process secondary structure from PDB - if selected, then structure information -read from PDB will be processed to derive secondary structure annotation. -

Use RNAView for secondary structure - if selected, the RNAView service will be -automatically called to derive secondary structure information. -

Add secondary structure annotation to alignment - if selected, PDB secondary structure -annotation will be shown on the alignment when available. -

Add Temperature Factor annotation to alignment - if selected, PDB Temperature Factor -annotation will be shown on the alignment when available. +read from PDB will be processed and annotation added to associated sequences. +

Use RNAView for secondary structure - if selected, the pyRNA RNAView service (https://github.com/fjossinet/PyRNA) will be +called to derive secondary structure information for RNA chains. +

Add secondary structure annotation to alignment - if selected, Jmol's implementation DSSP will be used to add annotation to polypeptide chains in the structure. +

Add Temperature Factor annotation to alignment - if selected, values extracted from the Temperature Factor +column for the backbone atoms in the PDB file will be extracted as annotation lines shown on the alignment.

Default structure viewer - choose JMOL or CHIMERA for viewing 3D structures.

Path to Chimera program - Optional, as Jalview will search standard installation paths for Windows, Linux or MacOS. If you have installed Chimera in a non-standard location, you can specify it here. Enter the full path to the Chimera executable program. diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 8fc557e..75a5c9c 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -24,14 +24,26 @@

Viewing PDB Structures

- -

Jalview can view protein structures associated with a sequence -via the "Structure→" submenu from a -sequence's pop-up menu.

-A Jmol viewer has been included since Jalview 2.3. Jalview 2.8.2 added support for Chimera, -provided this has been separately installed. Choice of default viewer is configurable in the Preferences Structure tab. - -

The following menu entries are provided for viewing structure data
+

+ Jalview can view protein structures associated with a sequence via the + "Structure→" submenu from a sequence's pop-up menu. +

+ The + Jmol viewer has been included since Jalview + 2.3. Jalview 2.8.2 included support for + Chimera, provided it is + installed and can be launched by Jalview. The default viewer can be + configured in the + Structure tab in the + Tools→Preferences dialog box. +

+ Structure data imported into Jalview can also be processed to display + secondary structure and temperature factor annotation. See the Annotation from Structure page for + more information. +

The following menu entries are provided for viewing structure data

The "Structure→View Structure→ submenu allows a single PDB structure to be chosen diff --git a/help/html/features/xsspannotation.html b/help/html/features/xsspannotation.html new file mode 100644 index 0000000..0dc7475 --- /dev/null +++ b/help/html/features/xsspannotation.html @@ -0,0 +1,90 @@ + + + +Annotation from 3D structure data + + +
+ Working with annotation from 3D structure data +
+
+ Jalview can process PDB data associated with sequences to display + values extracted from the Temperature Factor column for + corresponding sites, and secondary structure from DSSP or RNAView (as + appropriate). +
+
+ Extracting data from PDB files
Annotation is + created for structure files retrieved directly from the PDB loaded + from the file system (via the Structure→Associate + Structure...→From file option, or when displayed via the View + Structures Menu.
Structure annotation is not automatically + added to an alignment, but any available structure annotation rows for + the current selection or a particular sequence can be added via the Add + Reference Annotation in the Selection and Sequence + ID sub-menus of the Sequence ID Panel's popup menu.
Please + note:Protein structures are analysed + in situ, but Jalview employs a web service to process RNA + structures which can cause long delays if your internet connection is + slow. +
+
+ The Annotations + alignment menu provides settings useful for controlling the display + of secondary structure annotation. +
+
+ Shading sequences by associated structure annotation
The + annotation colouring dialog (opened by the Colour→By + Annotation option) allows sequences with associated secondary + structure data to be shaded according to secondary structure type. + Once the dialog is opened, select the Per Sequence option and + then choose Secondary structure from the dropdown menu.
When + colouring alignments by secondary structure, two modes can be + employed. The default is to shade sequences with the same colour as + the secondary structure glyph. If, however, original colours + is selected and another colourscheme has already been applied, then + only portions of the sequence with defined secondary structure will be + shaded with the previously applied scheme.
+
+
+ Configuration options for processing PDB files
+ Occasionally, you may wish to disable secondary structure processing. + Configuration options in the Structure tab in the Tools→Preferences + dialog allow the processing of structure data to be disabled, or + selectively enabled. For more information, take a look at the documentation for the structure panel. +
+
+ The display of secondary structure data was introduced in + Jalview 2.8.2, and is made possible by Jalview's use of Jmol's DSSP implementation, based on the + original Kabsch + and Sander algorithm ported by Robbie P. Joosten and + colleagues, and a client for Fabrice Jossinet's + pyRNA services that was developed by Anne Menard, Jim Procter and + Yann Ponty as part of the Jalview Summer of Code 2012. + +
+ + -- 1.7.10.2