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User Guide to Protean 3D — 17.4
  • 17.4
Table of Contents
Home Page
  • User Guide to Protean 3D — 17.4
    • User Guide to Protean 3D — 17.4
  • Welcome to Protean 3D
    • Separately-licensed services that integrate with Protean 3D
  • Protean 3D Tutorials
  • Protean 3D Interface
    • Welcome screen
    • Project tabs
    • Protean 3D toolbar
    • Views
      • Structure view
        • Try it! – Use the Structure view toolbar
        • Default colors and styles in the Structure view
      • Analysis view
        • Try it! – Apply tracks to the Analysis view
          • Part A: Apply and reorder tracks
          • Part B: Compare results from two tracks
          • Part C: Edit track options
          • Part D: Recolor tracks
        • Colors in the Analysis view
      • Sequence view
      • Report view
        • Composition report
          • Try it! – Study surface-exposed cysteines
        • Biophysical Properties report
        • Protein Design reports (Variants and Hot Spot Scan)
          • Filter hot spot scan results
        • NovaFold report
          • NovaFold Report: Molecule
          • NovaFold Report: Templates
          • NovaFold Report: Model Overview
          • NovaFold Report: Model ‘x’
            • Similar Experimental Structures
            • Predicted Binding Sites
            • Predicted Enzyme Function
            • Predicted Protein Function
          • Open a structure from the NovaFold Report
        • NovaDock report
          • NovaDock Report: Molecules
          • NovaDock Report: Model Overview
          • NovaDock Report: Model ‘x’
            • Models in Cluster
          • Open a structure from the NovaDock Report
      • NovaCloud Services view
      • Predictions view
      • Text view
      • Table view
      • Pairwise view
    • Panels
      • Explorer panel
        • Molecules section
          • Try it! – Use the Molecules section to select and hide a structural element
        • Surfaces section
          • Examples of surface types
      • Features panel
        • Try it! – Select and recolor a feature, and change feature options
        • (Feature) Options section
        • (Feature) Style section
      • Tracks panel
        • Track Options section
          • Biophysics tracks
            • Amphiphilicity (Eisenberg)
            • Charge Density (Lehninger)
            • Disorder (JRONN)
            • Flexibility (Karplus-Schulz)
            • Hydropathy – Hopp-Woods
            • Hydropathy – Kyte-Doolittle
            • Hydropathy – Parker
            • Secondary Structure – Chou-Fasman
            • Secondary Structure – Deleage-Roux
            • Secondary Structure – Garnier-Robson
            • Secondary Structure – Coiled Coil
            • Stability – Aliphatic Index
            • Stability – Instability Index
            • Stability – Isoelectric Precipitate
            • Surface Probability (Emini)
            • Transmembrane – Goldman-Engleman-Steitz
            • Transmembrane – TopPred
            • Transmembrane – von Heijne
          • Immunogenicity tracks
            • Antigenicity – Jameson-Wolf
            • Antigenicity – Welling
            • B-Cell Epitopes (DNASTAR)
            • MHC II Epitopes (Sette)
            • T-Cell Epitopes – AMPHI
            • T-Cell Epitopes – Rothbard-Taylor
          • Database tracks
            • Cleavage Sites (Proteases)
              • List of proteases
            • Domains & Sites (PROSITE)
              • Update the PROSITE database between releases
          • Modifications (SUMOylation) track
          • NovaFold-related tracks
          • Features (Annotated) tracks
      • Details panel
        • When no document or a blank document is open
        • A single residue or ligand
        • A molecule, feature or region
        • An entire structure
          • Try it! – View details about a structure
        • A selected region or strand
        • A group of structures
        • A track
        • A protease pattern or profile
        • An individual protease match
        • A PROSITE pattern or profile
        • An individual PROSITE match
        • A Protein Design result
        • The NovaFold report
        • The NovaDock report
      • Style panel
        • Rendering section
          • Try it! – Change the rendering of a structure
          • Examples of rendering styles
        • Color section
        • Sequence section
        • Lighting section
      • Models panel
      • Jobs panel
    • Motion Library
      • Try it! – Open a multi-model file from the Motion Library
  • Customize the Look and Layout
    • Customize the appearance and layout of views
    • Customize the layout of other window components
    • Save the layout and apply it to other projects
  • Open a File or Project
    • Open one or more local files
      • Change the default application for opening files
    • Type or paste a protein sequence
    • Open a PDB file when you know the ID
    • Open a PDB file when you don’t know the ID
    • Open a structure from the Motion Library
    • Open an existing Protean 3D project
  • Search for Sequences Online
    • Search for sequence matches (BLAST)
      • Search wizard: Query
      • Search wizard: Search
      • Search wizard: Options
      • Search wizard: Job
    • Search for text or accession number matches (Entrez)
      • Filter sequence search results
      • Filter text search results
      • Access ID dialog
  • Align Multiple Structures
    • Try it! – Align multiple structures using jFATCAT
  • Make a Selection
    • Try it! – Make a selection from the Sequence view
  • Work with Features
  • Overlay One Structure on Another
  • Create or Find Variants using Protein Design
    • Protein Design wizard: Workflow
    • Protein Design wizard: Structure
    • Protein Design wizard: Substitutes
    • Protein Design wizard: Options
    • Protein Design wizard: Job
    • View progress and see variant results
    • Use Protein Design for site-directed mutagenesis
    • Select Neighboring Residues
  • Evaluate Variants Produced in a SeqMan NGen Assembly
    • Part A: Create a templated assembly in SeqMan NGen
    • Part B (optional): Filter for variants of interest in ArrayStar
    • Part C: View variants in SeqMan Pro
    • Part D: View the protein structure in Protean 3D
  • Predict Structures, Antibody Interactions and Docking
    • Types of predictions
      • NovaFold: protein structure prediction
      • NovaFold AI: protein structure prediction
      • NovaFold Antibody: antibody interaction prediction
      • NovaDock: protein-protein docking
    • Run Nova applications within the Protean 3D interface
      • Run NovaFold through Protean 3D
        • NovaFold wizard: Sequences
        • NovaFold wizard: Options
        • NovaFold wizard: Submit
        • Try it! – Use NovaFold to predict a protein structure
      • Run NovaFold AI through Protean 3D
        • NovaFold AI wizard: Sequences
        • NovaFold AI wizard: Options
        • NovaFold AI wizard: Submit
        • Try it! – Use NovaFold AI to predict a protein structure with a cytosolic domain
      • Run NovaFold Antibody through Protean 3D
        • NovaFold Antibody wizard: Sequences
        • NovaFold Antibody wizard: Options
        • NovaFold Antibody wizard: Submit
      • Run NovaDock through Protean 3D
        • NovaDock wizard: Structures
        • NovaDock wizard: Options
        • NovaDock wizard: Submit
      • Try it! – Phage display assembly, translation and prediction
        • Part A. Assembly and trimming in SeqMan Ultra
        • Part B: Translation in SeqNinja
        • Part C: Alignment in MegAlign Pro
        • Part D: Structure prediction and docking in Protean 3D
    • Run Nova applications through the DNASTAR website
    • Run Nova applications locally
      • Install and set up the software
        • Uninstall the software
        • Reinstall the software
      • Prepare the input file(s)
      • Set up and run a prediction
        • Required commands
        • Required arguments
        • Optional arguments
        • Supplemental arguments
        • Stop a prediction in progress
  • Save and Export
    • Save a document
    • Export a still image
    • Export a structure file
    • Export an animation or video
    • Export data from the Text, Table or Pairwise views
    • Export a table of results from the Analysis view
    • Save or export a report
  • Close and Exit
  • Miscellaneous Tasks
    • Use basic editing commands
    • Set preferences
      • Set data preferences
      • Set Internet preferences
      • Set proteins preferences
      • Set temporary file preferences
    • Synchronize sequence updates between two Lasergene applications
    • Turn off usage logging
    • Use a mouse or trackpad with Protean 3D
    • Change the default print size
    • Prevent firewall issues when downloading from the Motion Library
    • Troubleshoot the error “A different version is running”
    • Troubleshoot blank Protean 3D window on Parallels Desktop
  • Appendix
    • Glossary
    • Supported file types
    • IUPAC codes
    • Installed Lasergene file locations
    • Useful links
    • Research references
    • Acknowledgements
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Miscellaneous Tasks

The following topics cover tasks and troubleshooting tips that do not fit into any of the main help categories:

General tasks Troubleshooting
Use basic editing commands
Set preferences
Synchronize sequence updates between two Lasergene applications
Turn off usage logging
Use a mouse or trackpad with Protean 3D
Change the default print size
Prevent firewall issues when downloading from the Motion Librar
Troubleshoot the error
Troubleshoot blank Protean 3D window on Parallels Desktop
Close and Exit
Use basic editing commands

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