This guide supports the Galter Library class called Structure Viewers. See our Classes schedule for the next available offering. If this class is not on our upcoming schedule, it is still available to you or your group by request.
There are many software packages for viewing molecular structures available for purchase or as free software downloads on the Web. Some structure viewers are good for viewing individual or multiple structures, while others provide more options for analysis of structure features. Others are best for creating publication-quality images.
This guide demonstrates the use of two structure viewers: NCBI's Cn3D and SwissProt's Deep View (also known as SPDBV). Users will learn where to download both viewers, how to use them for aligning similar structures, how to import a sequence to align to a structure and how to edit a structure's displayed characteristics.
The beginning of this guide offers a brief introduction to the Protein Data Bank, where users can download structure files.
The end of this guide provides users a link to download Pymol, a structure viewer that creates excellent publication-quality images. A list of other structure viewers is also located at the end of this guide.
The Protein Data Bank (PDB) is the official world wide repository for molecular structures.
Search the PDB by
This guide uses the example of "NK ly49" to search for natural killer receptor Ly49.
You can also click on the Advanced Search button and perform a guided search by specific field in the PDB record. The advanced search is also where you can paste a sequence and perform a BLAST against the structures in the PDB to see if a structure exists with similarity to your sequence.
In your search results page, you can refine your results by removing redundant structures using options to decrease sequence similarity. You can also sort your results by
Select a structure record by clicking on the PDB identifier or the description of the structure.
On the PDB structure summary
Structures can be searched in other databases besides the PDB. You can search for structures at the NCBI, as well. Cn3D is a structure viewer created by the NCBI. It is the default structure viewer for opening structures from NCBI's Molecular Modeling Database (MMDB).
To use Cn3D, you must first download the software onto your computer. Download links for Cn3D are located at multiple places in the structure search results, structure summary pages and from the NCBI's structure home page. Here is a direct link to the Cn3D download page.
From the results page, you can
From the structure summary page, you can click on the image of the structure to open it with Cn3D (if you have Cn3D installed on your computer--if not, you will be directed to the Cn3D download page).
For chain-specific structure comparisons, scroll down the page to the section showing the structure domain schematic images.
From this view you can
For this example, click on the Sequence D bar.
NCBI's VAST Related Structures
You are now on a page showing results from NCBI's VAST (Vector Alignment Search Tool) Related Structures search. On this, you will see a number of red bars aligned to your query sequence graphic. The results of this search are not limited to a specific family (such as natural killer cell receptors in this example) but will likely suggest members of a related fold class or superfamily.
To display multiple structures aligned to each other, click the checkboxes next to a few of the VAST results (the limit is 9) and click the View 3D Alignment button at the top of the page.
Viewing Structures with Cn3D
You are now viewing a multiple structure alignment in Cn3D. Cn3D will open two windows: a structure view window and a sequence view window. The style of the molecules is different from what you would see by opening any individual structure directly from its Structure Summary page at NCBI. The color shown is based on identity of amino acids, with red representing identical residues across the structures and cooler colors (such as blue) representing less similar amino acids. Note that, despite the low degree of sequence identity, the structural alignment is fairly good.
With Cn3D you can modify the view of your structure(s) in many ways:
From the Sequence/Alignment view window
Deep View has an interface that allows the user to make measurements, compute energy and change the structure of a molecule.
Importing Structures to Deep View
Open Deep View. You can close the About window so you only see the toolbar when you open the program. From the File menu, you can open any .pdb, mmcif or MOL (SDF) file that you have saved on your computer.
You can also use the Import command to search your computer for PDB files. The import window also allows you to use an Internet connection to search PDB for a particular PDB identifier. You can also search for PubChem IDs or paste a sequence in the window to model.
When you import a structure, sometimes structural data is incomplete, so Deep View will attempt to create side chains or other missing data. If this happens, a dialog window will open showing you all of the edits that the program made. You can close this window after viewing the information.
For this guide, use the PDB identifier 1P1Z and click the PDB file button in the Grab from server section of the menu. This is the natural killer cell receptor Ly49.
The Menu Bar in SPDBV
The pull-down menu bar in Deep View contains many options. There are too many options to list separately in this guide, so only a few will be demonstrated, but you can explore more functions as you become more familiar with the viewer.
The quick options are displayed as picture icons in the menu bar. These are some of the frequently-used features of the browser.
For more detailed descriptions of these quick button options, view the help document which can be accessed by clicking the small question mark (?) next to the buttons.
After you have opened a structure, open the Control Panel by selecting the Wind menu then selecting Control panel. From the control panel, you can make changes to entire chains or whole structures by using the columns.
The default structure view is a wire structure, so to view either space fill or ribbons, use the columns marked ::v or ribn to change the view. You can then set preferences for the ribbons using the Prefs menu in the viewer window.
Aligning Structures in Deep View
Import a second structure into your window using the Import option in the File menu. Try importing the PDB ID 1GZ2. This is a chicken egg shell protein (not a natural killer cell receptor).
When working with two or more structures, each structure is in a separate layer in the display. Toggle between layers by clicking on the structure ID in the control panel and switching to another layer by clicking its identifier.
To make your alignment easier to interpret, color the two structures by layer. In this view, 1P1Z is yellow and 1GZ2 is blue.
To align structures, you can use the button in the menu bar, but a better way to generate a structural alignment is to use the Fit menu.
Select Magic Fit, and a dialog box will pop up.
You can choose what parts of the structures to align, and which structure will be the reference layer. Click OK. Now your structures will align.
To make the two structures more easily viewed, remove the other chains from 1P1Z from the view and change the rendering to ribbons. You can do this from the control panel by selecting only chain D from 1P1Z, then selecting ribbons for both structures.
Then you can select Improve Fit from the Fit menu. Now you can see that some of the major structural features (beta strands and alpha helices) are aligned.
You can use the many options from the other menus to explore your structure.
Open the sequence alignment window by clicking on the Wind menu, then selecting Alignment. This way you can see residues selected in both the sequence and the structure.
Many other excellent structure viewers are available for free download by users.
Tutorials and help documents exist for PDB, Cn3D and Deep View.
Tutorials and help pages can also be found for most of the structure viewers listed in the section above. They usually can be accessed from the home pages for the viewers.
You can also get assistance in using many of these viewers from the Biosciences & Bioinformatics Librarian.
Updated: July 22nd, 2010 02:38