MSCI814 Module 11.

3D viewers, Cn3D and VAST (Vector Alignment Search Tool)

David Nelson March 17, 2016

LINKS FOR THIS MODULE

NCBI's CN3D tutorial

NCBI's VAST page

Molecular Modeling database MMDB.

Getting started with Cn3D

The Cn3D program for this class is located on the desktop. Click on Cn3D to start the program. The window contains a 3D helical structure that you can drag around with your mouse. Try it. Cn3D is NCBI's structure viewer program designed to view structure files in NCBI's Molecular Modeling database MMDB. The name has been changed just to Structure. In spite of the name, no theoretical models are included in MMDB/Structure. 3D structures have traditionally been deposited in PDB (The Protein Data Bank) and they still are. NCBI decided they needed links to structure from their many databases so they created MMDB. MMDB is made from PDB files and it is updated monthly. The Cn3D viewer cannot directly open and view PDB files. These must first be converted to ASN.1 format used in MMDB. However, this has already been done for all PDB files, so if you know the PDB code you can search for it in the MMDB window shown below.

The result will be a link to the MMDB page for this entry as shown below

Clicking on this link will take you to the MMDB page shown below

You can also reach this page by doing an Entrez search for a protein or gene name and clicking on any links to the structure database.


To view the 3D structure you need to click on the View 3D Structure button on the MMDB structure summary page(above). Depending on your computer and how it is configured, this may give you the option to choose an application to view the data, or you may have to download the datafile to your computer and open it with Cn3D. The computers in this lab will open the file directly. Click on view structure and select Cn3D as the viewer. You should see the following image. (The default view may be purple.)

You can drag this image with your mouse to twist and turn it. You should now be able to display the default view of any structure in MMDB. Remember, you can search MMDB for PDB codes.

Now that we are here, what can we do with Cn3D? We will give a quick tour of some of the features of Cn3D. The more detailed descriptions are in the Cn3D tutorial linked at the top of this page. You can download and install Cn3D on your own computer. MACs must have OSX for Cn3D version 4.x. I installed version 4.1 on my G4 MAC in about 5 minutes. It was very easy. The newest version is Cn3D 4.3. For details on how to install this see the Cn3D homepage This module continues on Page 2.