From: Jim Procter Date: Tue, 18 Nov 2014 09:44:36 +0000 (+0000) Subject: JAL-674 JAL-1512 JAL-1333 documentation X-Git-Tag: Jalview_2_9~149^2~1 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b8eecc11ecdeebc95f00014b5e588a583211ea32;p=jalview.git JAL-674 JAL-1512 JAL-1333 documentation --- 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