Frequently Asked Questions

Last modified: November 11, 2016

Section: 0 Basics

Subject: 0.1 What is VIPERdb?
Subject: 0.2 About the FAQ.

Section: 1 Navigation

Subject: 1.1 How to Navigate with the Top Menu?
Subject: 1.2 How to Navigate with the Pull Down Menu?
Subject: 1.3 How to Navigate with the PDB ID Search Box?

Section: 2 Contents of VIPERdb

Subject: 2.1 How Are Virus Entries Organized on VIPERdb?
Subject: 2.2 How Are Values/Calculations Determined for Each Entry?

Section: 3 Organization of Images on Info Pages

Subject: 3.1 Rendered Surface
Subject: 3.2 Ribbon Drawing of the Subunits
Subject: 3.3 Geometric Description of the Capsid
Subject: 3.4 Subunit Organization

Section: 4 Using/Extracting the Information

Subject: 4.1 How to Save?
Subject: 4.2 How to Enlarge?
Subject: 4.3 How to Compare 2+ Images?
Subject: 4.4 Where to Find Related Entries of a Virus?
Subject: 4.5 How to search for viruses within family/genus/T-number?

Section: 5 Lattice Types and Matrices

Section: 6 How to Generate a Complete Virus Particle?

Section: 7 Contact Us

Subject: 7.1 Have Questions for the Whole VIPERdb Team?

Section: 8 Resources

Subject: 8.1 Other Useful Links

Section: 9 Copyright & Disclaimer

Section: 0 Basics

Subject: 0.1 What is VIPERdb?
VIrus Particle ExploreER (VIPERdb) is a website and (behind the scenes) a curated repository and database of spherical virus structures and their structure derived results. All the virus structures available at the PDB are organized in a standard "VIPER" convention for the ease of their representation and computational analysis. Each virus structure (entry) is pictorially represented in terms of its surface topography and their subunit organization as well their subunit tertiary structures. Also each entry is analyzed in terms of their subunit-subunit contacts and association energies using the molecular mechanics program CHARMM. Currently, all entries in the database are of non-enveloped icosahedral viruses, but the work in underway to include helical viruses.

Subject: 0.2 About the FAQ
What kind of questions get included in the FAQ?
Any information that we think/find important! We will definitely include more questions that come from users of the VIPERdb site. So please send your questions to viper@scripps.edu

Who writes this?
This faq is written and maintained by the VIPERdb Team, with input from many current and past VIPERdb members. We are always happy to receive and accommodate any comments/corrections/add-ons. If you have any questions or comments, drop us a line at viper@scripps.edu or go to the contact page.

Section: 1 Navigation

Subject: 1.1 Navigating with the Top Menu

  • Main/Overview: Provides a brief description about the VIPERdb and description of VIPER convention/orientation.
  • Data: Provides links to list of viruses organized/grouped according to their family/genus/T-number etc.
  • Utilities: Provides links to Tools avilable at VIPERdb, from Oligomer generator to amino acid information. Please take time to explore.
  • Links: Links to useful/relevant sites.
  • Help: Useful help pages that includes information for both new and advanced users.
  • Find a Virus: Allows you to find a virus according to specifications and filters.

Subject: 1.2 Navigating With the Pull Down Entry Menus
There are two pull down menus, labeled 'X-RAY Entries' and 'CRYO-EM Entries' which list the viruses in our database. Left click on the pull down menus and select the virus entry that you would like to visit. Easier way to access these kinds of lists are from the main page menu (on the left) or from the data menu at the top, where the links to X-ray structures, cryo-EM structures, Model-based stats are provided.

Subject: 1.3 Navigating With the PDB ID Search Box
If you know the PDB-ID of your desired entry, enter it in the "Enter PDBID" window, it takes you to go straight to its info_page.

Section: 2 Contents of VIPERdb

Subject: 2.1 VIPERdb Entry Organization
The viruses can be grouped by their family,genus or quasi-symmetry/T-number, or whether it was determined by x-ray or cryo-EM

Subject: 2.2 Explanation for Calculations and Values
See our explanations page on calculations.

Section: 3 Organization of Images on Info Pages

On each individual virus/entry page, you will find two images in the (default) biodata tab: 1) ribbon diagram of the subunits (protomers) and surface representation of the entire virus. In the illustration-tab, there are 3 different representations are shown. You may click on each image to pull up the enlarged version of the image in a separate window.

Subject: 3.1 Rendered Surface
A surface rendering of the virus particle (biodata-lower right/illustrations-left) is generated using the TexMol program based on the atomic coordinates of the viral capsid proteins. The colors are depth cued according to the radius from blue to yellow. Thse renderings appear similar to those of cryo electron miscroscopy reconstructions at 20 Å resolution. The rendered surface representations readily brings out large-scale features such as "peaks" and, "canyons" and distinctive morphological units (e.g. hexamers and pentamers). It is convenient to compare different virus particles with these renderings as these images are generated on a relative scale. Thus it is possible to create a gallery/montage of viruses that are scaled to each other by combining these images with those from other viruses using the Gallary maker utilty.

Subject: 3.2 Ribbon Drawing of the Subunits
A ribbon drawing of the subunit(s) (biodata-top right) is provided for each unique gene product in the viral capsid. For a quasi-equivalent virus made of multiple copies of a single gene product, all the subunits that constitute the icosahedral asymmetric unit are shown (e.g., A, B and C subunits of T=3 capsids). For picornavirus and related capsids there will be three ß-sandwich domains. The ribbon drawings are colored with different tones to distinguish each unique subunit.

Subject: 3.3 Geometric Description of the Capsid
A geometric description of the capsid (illustrations-tab, middle diagram) shown with each virus was found to best describe the geometry of the subunit interactions. All of the viral capsids in this database display icosahedral symmetry. Some of the particles have the shape of an icosahedron, while others resemble other geometric solids that display icosahedral symmetry. These include truncated icosahedron, rhombic triacontahedron and dodecahedron. The fidelity of some viruses to these shapes is remarkable with dihedral angles between subunits conforming to within experimental error to the dihedral angles required to form the geometric solid.

Subject: 3.4 Subunit Organization
Under the Subunit Organization image (illustrations-tab, right diagram) is a pull-down menu that allows for selection of different views for the capsid rendered using Chimera. This includes various representations corresponding to different resolutions as well as inside view of the capsid, and views with ribbon or tube representations.

Section: 4 Using/Extracting the Information

Subject: 4.1 How to Save the Coordinates, Images etc.,
In the biodata-tab of each virus info page, there are links to the primary sequence of chains in the IAU, the PDB header file containing contextual info, the pdb to viper transformation matrix used to reorient the pdb coordinates, the transformed PDB coordinates, and coordinates for the full capsid, half capsid, and lattice. Click on any of these and the file will be displayed on the full screen. You may then use the save option on your browser if you would like to download them.

Header files: These are from the Protein Data Bank (PDB) site. They contain information about the virus, details about the structure determination amino acid sequence, secondary structure of the subunits etc.

Transformation Matrix: This file contains the matrix which takes the original PDB coordinates (from the PDB databank) and puts them in the standard orientation (Z35X looking down the z-axis).

Transformed PDB files: This file consists of the complete PDB entry, BUT CONTAINS THE TRANSFORMED COORDINATES, which corresponds to the particle at the origin (0,0,0) and placed in the standard orientation. Also co-ordinates of the hetero atoms and water molecules have been reorganized to better suit further analysis using CHARMM

Images: To save images: (right)click and hold on the image to be saved, you would see options: 1) view image 2) save image as etc., select the save option, a new window would pop up asking for the place to save, give a name with a proper extension that corresponds to the image format.

Subject: 4.2 Enlarging Images
Click on the any of the images on individual virus pages an enlarged image will pop up in its original size. If further enlargement is desired, you can try the zoom in option on your browser or save the images and view and enlarge them under any graphing programs or image viwers.

Subject: 4.3 Comparing Two or More Images
Visit the gallery_maker page, in which you can select any number of viruses and perform a side-by-side comparison of them according to their topology (to see relative sizes and surface features), ribbon subunits, capsomeres, or even their crystal contacts in the crystal lattice (available only for few entries).

Subject: 4.4 Viewing Related Entries of a Virus
Related entries can be accessed by clicking on the Related-Viruses tab on each info-page of a particular virus. For example, if you would like to find mutants or related entries of the bacteriophage MS2, just go directly to bacteriophage MS2 page and click on Related-Viruses tab.

Subject: 4.5 Searching For Viruses Within Family/Genus/T-number
You can search for viruses within family/genus or of a particular T-number, by using the links family-index, Genus-index or T-number index links under the "Data" pull down menu at the top. Then chose choose a family/genus/T-number of interest from the pull down menu at the top.

Specific search: input either virus name, PDB ID or T number and this search engine will bring you directly to the page you want.

General Search: If you don't know the exact information for certain virus or you would not be able to use the specific search engine. Then you can try to use this search engine with partial information (e.g., rhino for human rhino vius entries). It searches on the whole contents of this site and returns the list of links with related topics. From there you can find your way.

Section: 5 Lattice Types and Matrices

Viruses are often categorized by their T-number and P-numbers. The T-number describes the quasi symmetry present in the virus capsid, while the P-number describes the icosahedron's pseudo-symmetry. Follow this link for further information about lattice types.

There are sixty icosahedral matrices (Show me all 60!). By applying each of these matrices on the icoshedral asymmetric unit (IAU), complete virus capsids can be generated. Certain matrices from this list of sixty were used to generate capsomeres of virus particles. Please note that these matrices correspond to particles in the standard orientation. You may find the matrices that are required to generate capsomeres found in each of the following T-numbered capsids:

Section: 6 Steps to Generate a Complete Virus Particle:

Visit the Oligomer Generator and follow the instructions found there, or you can do it manually:

1. Download Transformed Coordinates
2. Download 60 Matrices
3. Apply 60 Matrices on Transformed Coordinates

Section: 7 Contact Us

Subject: 7.1 Have Questions for the VIPERdb Team?
Our email address is viper@scripps.edu.

Main | Data & Analysis | Utilities | Search | Contact Us | Help | Links | Mailing List | Cite VIPERdb | Disclaimer

©1998-2020. TSRI. All rights Reserved.