Analysis view

The Analysis view lets you quickly find regions of interest on a protein sequence. By default, the Analysis view is shown in the bottom left of the Protean 3D window. If the Analysis view is hidden or absent, you can display it using View > Analysis > Show. Alternatively, you can reset the entire Protean 3D window to the default layout using View > Document Layout > Restore DNASTAR Default Layout.

Once a sequence has been opened, the Analysis view shows a default selection of “prediction tracks” that can be used to evaluate secondary structural characteristics of a sequence. You can add more tracks to the Analysis view or hide unwanted tracks using the Tracks panel.

Selected features can be displayed along the same axis, if desired. Initially, a synopsis is displayed for each of the applied prediction tracks, while a consensus is displayed for the Feature/Annotation method. The synopsis or consensus is in the form of a colorful cartoon showing regional conclusions for the method or features.

Tracks are displayed as either line graphs or region plots, and all results are displayed on a common horizontal scale. Line graphs and region plots are two ways of visualizing the results of the same method. Line graphs are composed of a series of connected points, calculated at each residue and averaged over the window you specify. Region plots use the calculated data to make a yes/no decision, drawing a bar to represent a “yes” answer. The threshold for calling a region a distinct type may be adjusted when editing track options.

Columns represent clusters of identical sequences, while rows represent method calculations.

The following video is a brief introduction to the Analysis view:

Tasks that pertain to the Analysis view:

Task	How To
To open individual displays showing the “channels” or components that contributed to the synopsis	Click on the “plus sign” to the left of each synopsis or consensus.
To zoom in/out	Grab the green horizontal or vertical slider with your mouse and drag left/right or up/down to zoom in or out in the view. Alternatively, you can use any of the four Analysis > Zoom commands or use *Ctrl/Cmd+Shift+(arrow direction).
To expand or collapse a synopsis	Click the tree control on the left of the synopsis.
To change the amplitude of line graphs	Use Analysis > Plot in Peak Scale to set the amplitude of each line graph in the Analysis view to its own maximum range. Or use Analysis > Plot in Constant Scale to set the amplitude of each line graph in the Analysis view to the maximum range for the parent method. The latter is useful for comparing method results for two different assays.
To edit method options	See Track Options section.
To rearrange tracks	Select a synopsis. Drag the row and drop it in the desired position. All channels within the synopsis will move as a single group.
To collapse all channels on the view	Use Analysis > Collapse All Rows. This causes only the parent level synopses for each applied method to be displayed.
To copy a selection from the view	Right-click on the selection and choose Copy.
To create a new feature	Select the range for the feature, then right-click on the selection and choose New Feature.
To delete a feature	Right-click in the feature and choose Delete Feature.
To show/hide individual features	Check or uncheck them in the Features panel.
To create a virtual mutation within the current selection	Right-click on the selection and choose Create Variants. The Protein Design wizard opens with the Substitutes screen already populated for the selected range.
To make selections in the view	See Make a selection. To select everything except the current range, right-click on the selection and choose Invert Selection.
To remove chains/sequences from all synopses	Uncheck the corresponding box(es) in the Molecules section.
To change the color for a channel display	Select a channel (not a synopsis) and change the Fill color in the Color section. If you make a change to one item (e.g. an alpha helix), the color will change for all items in the view that share that class.
To toggle between displaying or hiding a ruler under each synopsis	Use the Analysis > Show Rulers or Analysis > Hide Rulers command or the Ctrl/Cmd+\ keyboard shortcut. Rulers display major ticks every ‘n’ residues, where ‘n’ is a multiple of 10 and varies depending upon the zoom level. Ruler numbering for sequences or synopses always starts at “1.” Numbering for select chains uses the position labels defined in the structure file.
To change the layout of the view or what is displayed in it	See Customize the look and layout.
To view tooltips (information balloons) about a feature or other item	Hover over it.
To restore the default display	Use Analysis > Reset Analysis View. This reverts to the default horizontal and vertical zoom level for the current window size, and collapses all rows.

*Note: When attempting to scroll left/right in this view, some Mac users may experience issues with the scroll bar. To easily correct the issue, see Fix issue with scrolling in the views.