X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fstructurechooser.html;h=f5f5916ed98d0517676a7e0b9807e1137fb982d4;hb=d0771875f23ab994c4f85fb6cd604378768df10e;hp=7dd69c1feada0d9de530c61055a6de7f5481c186;hpb=d709b26b0decca4a43788c225fef897818826ef9;p=jalview.git diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html index 7dd69c1..f5f5916 100644 --- a/help/html/features/structurechooser.html +++ b/help/html/features/structurechooser.html @@ -24,86 +24,104 @@ -

- Structure Chooser -

+ Structure Chooser +

- The Structure Chooser interface provides a smart technique for - selecting PDB structures to view in Jalview by querying readily - available meta-data of structures. The Interface can be invoked by selecting - the - "View Structure" option from a sequence's - pop-up menu. Some of the main - features it provides are listed below: -

Automatic discovery, retrieval and association of PDB entries - for an alignment's sequences
Visualisation of discovered structures' meta-data
Ability to configure the meta-data entries to visualise
Auto-selection of the best structure via filtering by the - available metric parameters in the meta-data (i.e. resolution, - quality etc).
Selection of multiple structures in a single operation

- Additionally, the Structure Chooser retains the following contemporary - features of Jalview: -

Manual association of PDB entries via entering the PDB Id or - From File
Ability to view cached PDB entries

+ The Structure Chooser interface provides a smart technique for + selecting PDB structures to view in Jalview by querying readily + available meta-data of structures. The Interface can be invoked by + selecting the + "3D Structure Data.." option from a sequence's + pop-up menu. Some of the main + features it provides are listed below: +

Automatic discovery, retrieval and association of PDB + entries for an alignment's sequences
Visualisation of discovered structures' meta-data
Ability to configure the meta-data entries to visualise
Auto-selection of the best structure via filtering by the + available metric parameters in the meta-data (i.e. resolution, + quality etc).
Selection of multiple structures in a single operation

+ Additionally, the Structure Chooser retains the following contemporary + features of Jalview: +

Manual association of PDB entries via entering the PDB Id + or From File
Ability to view cached PDB entries

- Associating PDB files with Sequences
- Discovery/Association of PDB entries to a sequence happens - automatically during the initialisation of the Structure Chooser - Interface. Jalview uses the sequence's ID to query the PDB Rest API, - provided by the EBI to discover PDB Ids associated with the sequence. + Associating PDB files with Sequences +
Discovery/Association of PDB entries to a sequence now + happens automatically during the initialisation of the Structure + Chooser Interface. Jalview uses the sequence's ID to query the PDB + Rest API provided by the EBI to discover PDB Ids associated with the + sequence. -

- Configuring displayed meta-data for Structures
- To configure the visible meta-data displayed for the discovered structures, click the 'Configure Displayed Columns' tab, then tick the options which you intend to make visible. +
+
+ Configuring displayed meta-data for Structures +
To configure the visible meta-data displayed for the + discovered structures, click the 'Configure Displayed Columns' tab, + then tick the options which you intend to make visible. -

- Auto-selection of best Structures -
Jalview can automatically filter and select the best structures using various metric categories avaialble from the meta-data - of the structures. To perform this simply select any of the following options from the drop-down menu in the Structure - Chooser interface: Best Uniprot coverage, Higest Resolution, +
+
+ Auto-selection of best Structures +
Jalview can automatically filter and select the best + structures using various metric categories avaialble from the + meta-data of the structures. To perform this simply select any of the + following options from the drop-down menu in the Structure Chooser + interface: Best UniProt coverage, Higest Resolution, Best Quality, + Highest Protein Chain etc. When the 'Invert' option is selected, + Jalview returns an inverse result for the current selected option in + the drop-down menu. +

- Best Quality, Highest Protein Chain etc. When the 'Invert' option is selected, Jalview returns an inverse result for the current selected option in the drop-down menu.

- - -
The screenshot above shows the Structure Chooser interface - along with the meta-data of auto-discovered structures for the sample - alignment. Note however that if no structures were auto-discovered, a - different interface for manual association will be invoked as seen in - the screenshot below. -

- -

- Manual selection/association of PDB files with Sequences -

To manually associate PDB files with a sequence, select any of - the follwing options listed below from the drop-down menu in the - interface: -

From File - You can load a PDB file from the - local machine or network and associate it with the selected sequence. - PDB files associated in this way will also be saved in the Jalview Archive file.
Enter PDB Id - Jalview will use the PDB Rest - API, provided by the EBI, to fetch the PDB file with the entered Id.
-
Cached PDB Entries - You can view PDB structures which have previously been downloaded/viewed using this option. Jalview caches previously downloaded PDB entries in the computer memory. However, if the project is saved before exiting Jalview, Jalview will serialize the cached entries to the file system.

+
The screenshot above shows the Structure Chooser interface + along with the meta-data of auto-discovered structures for the + sample alignment. Note however that if no structures were + auto-discovered, a different interface for manual association will + be invoked as seen in the screenshot below. +

+ +

+ Manual selection/association of PDB files with + Sequences +

To manually associate PDB files with a sequence, select any of + the follwing options listed below from the drop-down menu in the + interface: +

From File - You can load a PDB file from + the local machine or network and associate it with the selected + sequence. PDB files associated in this way will also be saved in + the Jalview Archive file.
Enter PDB Id - Jalview will use the PDB + Rest API, provided by the EBI, to fetch the PDB file with the + entered Id.
Cached PDB Entries - You can view PDB + structures which have previously been downloaded/viewed using this + option. Jalview caches previously downloaded PDB entries in the + computer memory. However, if the project is saved before exiting + Jalview, Jalview will serialize the cached entries to the file + system.

- The Structure Chooser interface was introduced in Jalview 2.x.x. - -

+ The Structure Chooser interface was introduced in Jalview + 2.9. +

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