Can Your Molecular Viewer Do This?

A Deep View of the NEW DeepView (Swiss-PdbViewer)
Version 4.0

"Between two evils, I always pick the one I never tried before."
Klondike Annie (Mae West)

Have you tried DeepView—lately?

FAST, FRIENDLY, MENU DRIVEN
All functions are available in menus and on intuitive pallettes. You need no programming skills, unless you want to write DeepView Scripts for automating repetitive tasks.

ALL OF YOUR MODELING TASKS IN ONE PROGRAM
If you now use a variety of programs for studying macromolecular models—analysis of structure and interactions, comparison of models, finding model errors, examining electron-density maps, computing surfaces and electrostatic potentials, minimizing energy, generating structural alignments, searching for functional sites, homology modeling, producing images for publication—you can now do ALL of these tasks, and more, with one powerful, fast, friendly, and easy-to-learn program: DeepView, available free (your favorite price) for Macintosh and Windows. In addition, you can automate many of your repetitive tasks with DeepView Scripts.

EXTENSIVE INTEGRATION WITH WEB SERVERS
Import from PDB, ExPDB, GenBank, UniProt, PubChem, Prosite. Submit and retrieve projects from SwissModel.

EASY-TO-FOLLOW TUTORIALS
For all DeepView functions, from the simplest viewing to sending and retrieving homology modeling projects, you will find clear tutorials to get you started, whether you are a true beginner or an experienced user needing more than your current program can do. Many of the tutorials are extensively student-tested.

Are you using several program, tools, or servers when you could do it all with just one?

DeepView 4.0 Features

View

• Easy mouse-driven rotation, translation, zoom, centering
• Wireframe, ball-and-stick, dotted surfaces, solid surfaces, ribbons
• Color by secondary structure, residue type, accessibility, chain, model, threading or force-field energy, B-factor or NMR-ensemble variation, sequence diversity, custom, many more
• View multiple models individually or superimposed, or flip through them
• View PDB file, click ATOM lines to jump to desired region in model
• Create images for publication (OpenGL or scenes for rendering in POV-Ray or MegaPOV)
• Improved and expanded handling of nucleic acids

Analyze and Compare Structure

• Superimpose and compare two, or many, models simultaneously
• Generate structural alignments
• Use interactive Ramachandran diagram, and save phi-psi statistics
• Search for functional signatures with Prosite
• Examine subunit contacts
• Find structural elements
• Find 3D motifs (Define 3d motif in a known structure, by selecting key residues. Then find and import proteins with identical or similar motifs from PDB.)
• Analyze ligand binding
• Measure bond lengths, angles, dihedral angles

Model

• Build protein models from scratch, starting from a sequence (amino acids or codons)
• Build loops, break and ligate backbone, add termini, add hydrogens
• Build oligomeric proteins from protomers
• Build unit-cell contents by crystallographic symmetry
• Search ExPDB and UniProt by BLAST
• Search ExPDB via SwissModel for homology-modeling templates
• Import and align templates, and generate structural alignments
• Thread raw sequence onto templates
• Minimize energy (GROMOS)
• Submit modeling projects to SwissModel, and retrieve final model, all within DeepView
• Switch between SwissModel Workplace and DeepView at any point in a modeling project

Judge Model Quality

• Search for protein problems—clashes, buried sidechains lacking expected H-bonds, out of Rama-allowed zones, residues in unlikely environments
• Color by B-factor or RMS deviation within an NMR ensemble
• Import and view electron-density maps
• Refit models into electron density
• Minimize energy in modified areas of models (GROMOS)

Compute, Import, and View Surfaces

• van der Waals surface
• Molecular and accessible surface (SPDBV, MSMS, GRASP)
• Electrostatic potential (potential surface or mapped onto molecular surface: SPDBV, GRASP/DELPHI)
• Election density (DN6, CCP4, XPLOR)
• View all surfaces dotted, solid, or transparent

Import, Edit, and Convert Model Files

• Load PDB, MOL (SDF), and (eventually) mmCIF files
• Save all file types as PDB
• Import PDB, ExPDB (modeling templates or BLAST results from SwissModel Workspace), modeling results (SwissModel Workspace), motif-search results (Vital-IT), ProSite results and definitions, electron-density maps (EDS), compounds (PubChem), sequences to model (ExPASy or NCBI), and others to come
• Add and delete residues and termini
• Change residue numbers, ligand names, chain designations, model names
• Merge models to build oligomers or protein-ligand complexes
• Fit residues or ligands into electron density and save modified model
• Save sequence (FASTA) or alignment (gapped FASTA) as amino acids or codons

Automate

• Write or import DeepView Scripts to carry out repetitive work on one or many models (useful scripts and examples provided)

LEARN Quickly and Painlessly!

• Learn how to use all DeepView tools from extensive tutorials.
  
• Student-tested beginning tutorials for users who are new to molecular graphics, or even new to proteins.
• Advanced tutorials introduce DeepView's most powerful features.

Can your current modeling program do all this?

Get to know DeepView. Version 4.0 available NOW.

Happy Modeling!

Updated 2008-06-25

The Molecular Level