Details
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Type:
Epic
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Status: Open
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: 3.0
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Component/s: Scriptable API, Structures
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Labels:None
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Epic Name:jmolJalviewInterop
Description
In traditional Jalview use, Jmol is a subsidiary viewer controlled by Jalview. This situation has begun to change with the use of the Jmol data api to process macromolecular coordinate data files, and in version 3 of Jalview, we should consider alternate patterns of use where Jmol is used to import and manipulate data displayed by Jalview.
Principal issues:
1. It should be possible to open a Jmol window without any 3D data already imported into Jalview.
e.g. provide an 'open Jmol' top level menu entry.
2. Data imported into Jmol should be displayed in one or more linked Jalview alignment windows.
e.g. load ... operations that result in new structures in a Jmol view can be added to existing Jalview alignment windows, or opened in a new alignment window.
3. Manipulations to the data and selection state in Jmol should result in updates to linked Jalview windows.
e.g. a. if the user edits or removes structure data, the data should disappear from linked views in Jalview.
e.g. b. selections and named groups should be shown in linked alignment windows.
Principal issues:
1. It should be possible to open a Jmol window without any 3D data already imported into Jalview.
e.g. provide an 'open Jmol' top level menu entry.
2. Data imported into Jmol should be displayed in one or more linked Jalview alignment windows.
e.g. load ... operations that result in new structures in a Jmol view can be added to existing Jalview alignment windows, or opened in a new alignment window.
3. Manipulations to the data and selection state in Jmol should result in updates to linked Jalview windows.
e.g. a. if the user edits or removes structure data, the data should disappear from linked views in Jalview.
e.g. b. selections and named groups should be shown in linked alignment windows.