New Genome Browser (NGB) - a Web - based NGS data viewer with unique Structural Variations (SVs) visualization capabilities, high performance, scalability, and cloud data support
We should expand the Molecular viewer functionality by the following features:
ability to change the view (display) mode for the model
ability to change the color scheme for the model
ability to change the model view in an advanced regimen (e.g. change the display mode not for whole model but only for the selected parts, or change the "material" of the model, etc.)
saving the full model state when saving the session
Approach
View mode
We should add the ability to change the view (display) mode for the displaying model.
For that:
add the corresponding button at the Molecular viewer panel, e.g.:
by click this button, the list with possible display modes shall appear, e.g.:
user can click any item in the list and the selected mode should applied to the model, e.g. if the VDW mode was selected:
Selected display mode should be applied as well to other structure or chain of the model if it is selected.
By default (if the model is just opened or re-opened), the "Cartoon" display mode should be set.
Possible display modes should be taken from here.
Color scheme
We should add the ability to change the color scheme for the displaying model.
For that:
add the corresponding button at the Molecular viewer panel, e.g.:
by click this button, the list with possible color schemes shall appear, e.g.:
user can click any item in the list and the selected scheme should applied to the model, e.g. if the Residue scheme was selected:
Selected color scheme should be applied as well to other structure or chain of the model if it is selected.
By default (if the model is just opened or re-opened), the "Structure" color scheme should be set.
Possible display modes should be taken from here.
Advanced regimen
We should add the ability to edit the model in the advanced regimen - support all abilities that miew.app allows to perform.
In terms of GUI, it should look like:
user opens the model in the NGB Molecular viewer panel
if user wants to use all abilities to edit the model view - he/she shall click the corresponding button at the Molecular viewer panel (e.g. "Advanced edit"):
the model should be opened in the separate form/tab or pop-up, where miew.app is hosted
user configures the model view in the advanced regimen
user ends to configure the view, closes the advanced regimen form/tab or pop-up and return to the NGB Molecular viewer panel - the model should have all the same view (with all the set customized settings) as it was in the advanced regimen
Saving in the session
If user saves the session while the Molecular viewer panel is opened - the full state of the opened model should be saved in the session:
model, selected structure and chain
view of the model - display mode and color scheme
the set angle
the set zoom level
So, if user will open such session - the Molecular viewer panel should be opened with the full same model image as it was saved.
NShaforostov
commented
2 years ago
Background
We should expand the Molecular viewer functionality by the following features:
Approach
View mode
We should add the ability to change the view (display) mode for the displaying model. For that:
VDWmode was selected:Selected display mode should be applied as well to other structure or chain of the model if it is selected. By default (if the model is just opened or re-opened), the "Cartoon" display mode should be set. Possible display modes should be taken from here.
Color scheme
We should add the ability to change the color scheme for the displaying model. For that:
Residuescheme was selected:Selected color scheme should be applied as well to other structure or chain of the model if it is selected. By default (if the model is just opened or re-opened), the "Structure" color scheme should be set. Possible display modes should be taken from here.
Advanced regimen
We should add the ability to edit the model in the advanced regimen - support all abilities that miew.app allows to perform. In terms of GUI, it should look like:
Saving in the session
If user saves the session while the Molecular viewer panel is opened - the full state of the opened model should be saved in the session:
So, if user will open such session - the Molecular viewer panel should be opened with the full same model image as it was saved.