Molecules section

The Molecules section is located in the Explorer panel lists the structures and components (chains, ligands and water) for each structure in the current document. If you display/hide/select items in the Molecules section, these choices are simultaneously displayed/hidden/selected in the other Protean 3D views.

Opening the Molecules section:

Do any of the following:+

• Click the expand bar entitled “Molecules”
• Use View > Explorer > Molecules
• Press Ctrl+Alt+M (Windows) or Option+Cmd+M (Macintosh)

*Note: The Molecules section can only be opened if a document is open in the Protean 3D application window.

Using the Molecules section:

All independent protein chains, DNAs, RNAs, small molecules and metal ions bound to the complex are listed separately in tree format. Expand the arrows to reveal the elements of each structure. Each molecule is named by its common chemical name and by the chemical formula, where possible.

Chain names and details are taken directly from the PDB file. Protean 3D automatically generates chain names when none are available in the file, as is often the case in ATOM-only files.

• When viewing a sequence file, such as a GenBank file, the Molecules section displays only the file name and a list of sequence or locus names.

• When viewing a multiple-structure document, including prediction model/template alignments launched from the NovaFold Report, each structure or template protein fragment appears as a separate section.

Icons in the Molecules section:

Icon	Function
	Denotes a protein chain.
	Denotes a DNA chain.
	Denotes an RNA chain.
	Denotes a ligand.
	Denotes water.
	A checkmark denotes that the element is currently displayed in the Protean 3D views . All checkboxes are initially checked by default, but can be manually unchecked to hide various structural elements in the Structure view and to hide sequence in the Sequence view. Expand arrows to the left of the checkboxes can be used to reveal/hide additional structural elements. Expand arrow icons vary by operating system and may not be visible unless the mouse is hovering above them.