Export an animation or video

Save and Export » Export an animation or video

To save an animated sequence in QuickTime Movie (.mov) or .avi format, choose File > Export Movie. Both formats are saved to play back at 6 frames per second (166 ms/frame), which is one-quarter the speed of standard television programs and films. This speed was…

Save and Export

Save and Export

Click on one of the links below to learn how to: Save a document Export a still image Export a structure file Export an animation or video Save or export a report

When no document or a blank document is open

Analyze a Sequence or Structure » Protean 3D windows, views, panels and tools » Panels » Details panel » When no document or a blank document is open

When no document or a blank document is open, the Details panel displays information for getting started in Protean 3D. Click on the links to open a file, the Motion Library, or a recent document; or to predict protein folding with NovaFold; or to watch a training…

Welcome to Protean 3D

Welcome to Protean 3D

Protean 3D is Lasergene’s application for exploring macromolecular structure, motion, and function. Rich, synchronized graphical views allow you to see the 3D molecular structure, the annotated sequence, and the analysis of applied prediction methods…

Useful links

Appendix » Useful links

Name and Link Description CATH Protein Structure Classification Database A curated classification of protein domain structures. Each protein is assigned to a homologous superfamily (group of domains related by evolution). The CATH…

Work with Features

Work with Features

The following video is a brief introduction to working with features in Protean 3D: For detailed information, see the table below: Task How To To control which features are displayed in the Sequence and Analysis views See Features panel.…

View NovaFold results

Explore Protein Folding, Antibody Interactions, and Protein Docking » View NovaFold results

When you open a completed NovaFold prediction (.novafold) in Protean 3D, a specialized Report view contains detailed results about the prediction. The sections of the NovaFold Report are: Molecule Templates Model Overview Model ‘x’ and its…

Lighting area

Optimize the Protean 3D Interface » Protean 3D windows, views, panels and tools » Panels » Style panel » Lighting area

The Lighting area, located in the Style panel, allows you to change lighting characteristics of the Structure view. Up to three “directional” lights may be deployed, in addition to displaying “ambient” light. The following video shows the…

NovaDock – Protein docking

Explore Protein Folding, Antibody Interactions, and Protein Docking » NovaDock – Protein docking

NovaDock is DNASTAR’s protein docking application. DNASTAR provides NovaDock as a cloud-based, separately licensed service within Protean 3D™. NovaDock’s algorithm is based on SwarmDock, developed in Dr. Paul Bates’ laboratory at the Cancer…

Align Multiple Structures

Align Multiple Structures

Homologous proteins often have similar structures. A structure alignment attempts to identify these similarities by comparing the shape and 3D conformation between two structures. Unlike simple superposition methods, structure alignments do not require prior knowledge…

NovaFold Antibody – Antibody interactions

Explore Protein Folding, Antibody Interactions, and Protein Docking » NovaFold Antibody – Antibody interactions

NovaFold Antibody is specifically designed to generate models of antibodies and antibody fragments (Fv, Fab, VH, sdAb) and, with the use of NovaDock, predict the structure of antibody-antigen complexes. DNASTAR provides NovaFold Antibody as a cloud-based,…

B-Cell Epitopes (DNASTAR)

Optimize the Protean 3D Interface » Protean 3D windows, views, panels and tools » Panels » Tracks panel » Track Options area » Immunogenicity tracks » B-Cell Epitopes (DNASTAR)

The B-Cell Epitopes (DNASTAR) prediction track uses a bioinformatics approach that uses experimental antibody recognition data. For a set of peptides provided by NeoClone® Biotechnology International, LLC (Madison, WI USA), the antigenicity of each peptide was…

Shared toolbar

Optimize the Protean 3D Interface » Protean 3D windows, views, panels and tools » Shared toolbar

The shared toolbar is located below the Protean 3D menus, and can be shown or hidden using the Controls > Show/Hide Toolbar command. The following video demonstrates some of the shared toolbar functions: The first two tools on the left of the toolbar affect the…

Rendering area

Optimize the Protean 3D Interface » Protean 3D windows, views, panels and tools » Panels » Style panel » Rendering area

The Rendering area 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…

Domains & Sites (PROSITE)

Optimize the Protean 3D Interface » Protean 3D windows, views, panels and tools » Panels » Tracks panel » Track Options area » Database tracks » Domains & Sites (PROSITE)

The Databases – Domains & sites (PROSITE) track searches chains against common patterns found in the PROSITE database (installed with your software). When you apply the method, Protean 3D will search the protein sequence against the pattern library and display…

Motion Library

Optimize the Protean 3D Interface » Protean 3D windows, views, panels and tools » Motion Library

The Motion Library consists of over 500 animated and annotated macromolecular motions illustrating structural conformational changes. The intermediate structures in the animation are an interpolation between two experimentally-determined protein conformations…

Cleavage Sites (Proteases)

Analyze a Sequence or Structure » Protean 3D windows, views, panels and tools » Panels » Tracks panel » Track Options area » Database tracks » Cleavage Sites (Proteases)

The Cleavage sites (Proteases) track predicts cleavage sites for proteases (also termed peptidases or proteinases) and chemicals in a protein sequence using known proteolytic signatures. When you apply Cleavage sites (Proteases) to the Analysis view, Protean 3D…

Surfaces area

Optimize the Protean 3D Interface » Protean 3D windows, views, panels and tools » Panels » Explorer panel » Surfaces area

The Surfaces area is located in the Explorer panel and is used to create molecular surfaces for selections in the Structure view. The following video shows the Surfaces area in action: Opening the Surfaces area: Do any of the following: Click the expand bar…

Analysis view

Analyze a Sequence or Structure » Protean 3D windows, views, panels and tools » Views » Analysis view

Protean 3D’s “prediction tracks” can be used to evaluate secondary structural characteristics of a sequence. The Analysis view displays a graphical representation of all prediction tracks that have been applied to the active sequence or structure using the Tracks…