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Explorer panel
Protean 3D Interface » Panels » Explorer panel
The Explorer panel, represented by a compass icon (), includes two expandable sections that allow you to view, select or hide structural elements and to apply surfaces to the structure. Opening the Explorer panel: Do any of the following: Click on the Explorer…
Molecules section
Protean 3D Interface » Panels » Explorer panel » 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…
Try it! – Use the Molecules section to select and hide a structural element
Protean 3D Interface » Panels » Explorer panel » Molecules section » Try it! – Use the Molecules section to select and hide a structural element
This tutorial shows how to select a particular structural element from the Molecules section. Within Protean 3D, choose File > Open from PDB. You may initially see a yellow warning icon () prompting you to type in a valid ID. Type 7TIM into the text box. …
Try it! – View details about a structure
Protean 3D Interface » Panels » Details panel » An entire structure » Try it! – View details about a structure
This tutorial demonstrates how to use the Details panel to view information about a structure or sequence. Within Protean 3D, choose File > Open from PDB. You may initially see a yellow warning icon () prompting you to type in a valid ID. Type 7TIM into the text…
Structure view
Protean 3D Interface » Views » Structure view
The Structure view displays a physical representation of the molecule in your structure file. By default, the Structure view is shown in the upper left of the Protean 3D window. If the Structure view is hidden or absent, you can display it using View > Analysis > Show.…
Panels
Protean 3D Interface » Panels
Settings panels allow you to optimize the look, contents and layout of the Protean 3D view. To learn what can be done within each panel and their expandable sections, click the links below. Panel name Sections within the panel Explorer …
Surfaces section
Protean 3D Interface » Panels » Explorer panel » Surfaces section
The Surfaces section is located in the Explorer panel and is used to create molecular or solvent-accessible surfaces for selections in the Structure view. The following video shows the Surfaces section in action: Opening the Surfaces section: Do any of the…
Try it! – Study surface-exposed cysteines
Protean 3D Interface » Views » Report view » Composition report » Try it! – Study surface-exposed cysteines
Surface-exposed cysteine residues are of interest in industrial applications because they tend to form disulfide bridges with other molecules, disrupting the stability of the original protein. The following example shows one way to study cysteines in a protein…
Open an existing Protean 3D project
Open a File or Project » Open an existing Protean 3D project
To open an existing Protean 3D project (.msa): Use the File > Open command, select the Open a file tool (), or press Ctrl/Cmd+O. For an additional shortcut to this command, see The Welcome Screen. Once a project is open in Protean 3D, you can open additional files…
Labels section
Protean 3D Interface » Panels » Explorer panel » Labels section
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…
Rendering section
Protean 3D Interface » Panels » Style panel » Rendering section
The Rendering section is located in the Style panel, and provides options for customizing the look of the Structure view. The following video is a brief walkthrough showing how to apply a different rendering style to highlight features of interest: Opening the…
Search wizard: Query
Search for Sequences Online » Search for sequence matches (BLAST) » Search wizard: Query
The Query screen is the first of four screens in the BLAST Search wizard. The Query screen is where you add the query sequence, i.e., the sequence for which you wish to locate matches in the NCBI BLAST database. At the top of the screen, next to “Search…
Part A. Assembly and trimming in SeqMan Ultra
Predict Structures, Antibody Interactions and Docking » Run Nova applications within the Protean 3D interface » Try it! – Phage display assembly, translation and prediction » Part A. Assembly and trimming in SeqMan Ultra
This section of the tutorial describes the procedure for working with .abi files, by far the most common file type used in this workflow. (NGS files are handled differently; please contact us for instructions.) In this section, you will use SeqMan Ultra to de novo…
Try it! – Use NovaFold AI to predict a protein structure with a cytosolic domain
Predict Structures, Antibody Interactions and Docking » Run Nova applications within the Protean 3D interface » Run NovaFold AI through Protean 3D » Try it! – Use NovaFold AI to predict a protein structure with a cytosolic domain
In this tutorial, you will download the protein sequence of an adhesion GPCR with cytosolic domains. These domains cannot be seen using x-ray crystallography but can be accurately predicted using NovaFold AI. The tutorial is separated into four parts for clarity, but…
Try it! – Use NovaFold to predict a protein structure
Predict Structures, Antibody Interactions and Docking » Run Nova applications within the Protean 3D interface » Run NovaFold through Protean 3D » Try it! – Use NovaFold to predict a protein structure
The following tutorial is separated into four parts for clarity, but the entire tutorial only requires about 15 minutes of “hands-on” time. Between Parts A & B, there is also a 12-24 hour wait for the prediction to take place. Part A: Use NovaFold to…
Try it! – Align multiple structures using jFATCAT
Align Multiple Structures » Try it! – Align multiple structures using jFATCAT
This tutorial demonstrates how to align two structurally homologous protein files within a single document. This technique is useful for discovering similarities and differences between related structures. The files used in this tutorial will be opened from the RCSB…