Index

• Introduction
  • What does Cn3D do?
  • Downloading and installing Cn3D
  • Document conventions
  • Literature references
• Retrieving individual structures (MMDB)
  • From an Entrez literature search
  • From an Entrez sequence neighbor
  • From a BLAST search
  • From a known PDB identifier
• Viewing individual structures in Cn3D
  • Basics of Cn3D controls
    • The structure window main menu
    • The style panel
  • Cn3D's sequence viewer
• Retrieving structure alignments (VAST)
• Viewing structure alignments in Cn3D
  • Cn3D's alignment viewer
  • Cn3D's alignment model
• Imports and conservation
  • Importing sequences and structures
  • Visualizing sequence conservation
• Annotating a structure
  • Backbone and termini labels
  • User-defined styles
• Saving structures and images
  • Using Cn3D for interactive figures
• Advanced topics
  • Animation controls
  • Visualizing crystallographic disorder
  • Pattern searching
  • Importing user PDB files
• Alignment editing
  • Using the editor
  • Correcting alignment errors
  • Merging sequences into a multiple alignment

Introduction

This is a tutorial for Cn3D 4.1. It is intended as a guide to the major features of Cn3D for both new and experienced users. New users may wish to learn to use the program by reading this document in order; experienced users may wish to jump to sections of particular interest using the above index and hyperlinks within the text.

This tutorial is not an exhaustive explanation of all the program's features; there is a built-in help document that explains Cn3D's user interface and features in detail - see Help:Commands.

What does Cn3D do?

Cn3D is a visualization tool for biomolecular structures, sequences, and sequence alignments. What sets Cn3D apart from other software is its ability to correlate structure and sequence information: for example, a scientist can quickly find the residues in a crystal structure that correspond to known disease mutations, or conserved active site residues from a family of sequence homologs. Cn3D displays structure-structure alignments along with their structure-based sequence alignments, to emphasize what regions of a group of related proteins are most conserved in structure and sequence. Also included are custom labeling features, high-quality OpenGL graphics, and a variety of file exports that together make Cn3D a powerful tool for literature annotation. Cn3D is typically run from a WWW browser as a helper application for NCBI's Entrez system, but it can also be used as a standalone application.

With version 4, Cn3D is now a complete multiple alignment editor as well, and includes algorithms for aligning sequences to other sequences and to structures. You can now create and even annotate multiple alignments. Cn3D is used as the primary alignment curation tool for the CDD project.

Downloading and installing Cn3D

Cn3D is available for Windows, Macintosh, and various UNIX platforms. These pages include instructions for downloading and installing Cn3D, and for configuring WWW browsers to use Cn3D as a helper application.

Document conventions

Screen shots of the Cn3D and sequence windows are provided at various intervals to exemplify the concepts described; they will appear as thumbnail images linked to full-size screen shots. Note that the full-size images are stored in PNG format - depending on the browser used, a PNG-capable helper application may be required to view them. The Windows version of Cn3D was used to create these images, but aside from platform look-and-feel differences in user interface and window borders, the images will look largely the same on any platform.

When referring to specific elements of the user interface (pull down or popup menus, buttons, etc.), this document will use boldface type with colons separating the ordered mouse-actions needed to access that feature. For example, Style:Edit Global Style:Details:Tube Radius means go to the "Style" pull-down menu (in the structure window), select the "Edit Global Style" item. A tabbed control panel comes up; select the "Details" tab, then look for the "Tube Radius" control.

Literature references

In order to make this tutorial interesting as well as informative, we have tried to use notable examples from current literature. Most of the examples center on the human PTEN protein (Lee et al., 1999), a tumor suppressor found mutated in many cancers (for a review, see Di Cristofano and Pandolfi, 2000).

Below is a complete list (with links into Entrez) of all literature cited in the preparation of this tutorial.

1. Di Cristofano A, Pandolfi PP. The multiple roles of PTEN in tumor suppression. Cell 2000 Feb 18; 100(4):387-90. (Entrez)
   
   
2. Lee JO, Yang H, Georgescu MM, Di Cristofano A, Maehama T, Shi Y, Dixon JE, Pandolfi P, Pavletich NP. Crystal structure of the PTEN tumor suppressor: implications for its phosphoinositide phosphatase activity and membrane association. Cell 1999 Oct 29; 99(3):323-34. (Entrez)
   
   
3. Liaw D, Marsh DJ, Li J, Dahia PL, Wang SI, Zheng Z, Bose S, Call KM, Tsou HC, Peacocke M, Eng C, Parsons R. Germline mutations of the PTEN gene in Cowden disease, an inherited breast and thyroid cancer syndrome. Nat Genet. 1997 May; 16(1):64-7. (Entrez)

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