The Labels section is located in the Explorer panel and is used to create a visual label for selections in the Structure view.

To open the Labels section, click the expand bar entitled Labels or use View > Explorer > Labels. Note that the Labels section is only functional if the project contains a protein structure rather than a sequence.

Columns in the Labels section:

Column Name Description
Name By default, the Name field is automatically assigned based on the order in which labels were created. The default names are New 1, New 2, New 3, etc. If the Domain is Editable, then the Name column can be manually edited as described in the table below.
Domain Displays the current Label domain for the label. By default, the domain is Editable unless otherwise specified. See the table below for more information.
Text Initially displays descriptive text pertaining to the labeled selection. For example, if you made a selection by clicking on the Name or Details columns of the Molecules section, the text from those columns is used. If you selected a structural feature in the Sequence view, the text will consist of the feature type followed by its number along the sequence, e.g., Helix 8 for the eighth helix to occur on the sequence. If the Domain is Editable, then the Text column can be manually edited as described in the table below.
Details Displays the structure, chain, and residues in the labeled selection, separated by colons, e.g., 4HHB:A(119..136).

Tasks related to the Labels section:

Task How To
Specify the item you wish to label Do any of the following:

  • Double-click on a residue in the Structure view

  • Click on a component in the Sequence view (e.g., a residue, binding site, helix, etc.)

  • Click on a component in the Molecules section (e.g., a structure, chain, or ligand)
Create a label for the currently selected item Do either of the following:

  • Click on the Create a new label tool () to create the default label type based on your selection (recommended).

  • Click on the arrow to the right of the tool to manually specify the domain (type) of label to create: Atoms, Residues, Chains, or Editable. The label domain can be changed later, as described further down this table.
Specify a label domain (type) for the selected label The label domain (see types, above) affects which options are enabled in the Options section. Unless otherwise specified, the label domain is set to Editable by default. Specific domains (Atoms, Residues, Chains) can be assigned in any of three ways:

  • Protean 3D can assign the domain automatically based on what you selected before pressing the Create a New Label tool ().

  • You can use the the drop-down menu to the right of the Create a New Label tool to assign or change the domain type.

  • You can use the Label domain drop-down menu in the lower part of the Labels section to assign or change the domain type.
Choose what information is displayed as part of the label Check boxes in the Options section to chose components how the label is displayed. Available options depend on which type of Label domain is currently selected (see row above).

  • Coordinates – Check this box to append a colon and the residue’s sequence position onto the label (e.g., to display Ala:19 instead of Ala).

  • Arrowhead – To add an arrowhead to the line connecting the label to the structure component.

  • 1-letter – By default, 3-letter IUPAC codes are displayed for each residue. Check this box to instead display 1-letter codes.
Change the name or text for an existing label If the Domain is Editable, then the Name and Text fields can be edited. To do this, double-click on a cell in the Name or Text column and type in the desired text.
Specify the font, style, and text size for all labels Font specifications apply to all labels, not to individually selected labels. To customize the font, use the three drop-down menus under Font. As you change these options, the display changes to reflect the number of angstroms (Å) represented by the label. To change the text outline (“stroke”) and fill colors, click the boxes to the right of Fill and Stroke and choose the desired color from the color picker. By default, labels are shown in Arial Regular 256 pt with white fill and black stroke.
Toggle between displaying/hiding an existing label Check or uncheck the box at the left of the row.
Toggle between displaying/hiding all labels Check or uncheck the box on the left of Name in the header.
Delete a selected label Select the label you want to remove and use the Delete selected labels tool (). This deletes the currently selected row from this section and removes the label from the Structure view.

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