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Frequently Asked Questions

Last modified: March 24, 2004 [Contents]

Section: 0 Basics

Subject: 0.1 What is VIPERdb?
Subject: 0.2 History of VIPERdb
Subject: 0.3 About the FAQ.

Section: 1 Navigation

Subject: 1.1 How to Nagigate with the Menu at the Left Frame?
Subject: 1.2 How to Navigate with the Pull Down Menu?

Section: 2 Contents of VIPERdb

Subject: 2.1 Alphabetically ordered by the VIRUS names
Subject: 2.2 Organization by quasi and pseudo symmetry
Subject: 2.3 Calculations

Section: 3 Organization of Images

Subject: 3.1 Rendered Surface
Subject: 3.2 Ribbon Drawing of the Subunits
Subject: 3.3 Geometric Description of the Capsid
Subject: 3.4 Capsomeres Depicted as C-alpha Drawings of Subunits

Section: 4 Using the information

Subject: 4.1 How to Save?
Subject: 4.2 How to Enlarge?
Subject: 4.3 How to Compare Two Images?
Subject: 4.4 Where to Find Mutants and Related Entries for a Virus?
Subject: 4.5 How to Search the Contents of This Site?

Section: 5 Lattice Types and Matrices

Section: 6 Generating Complete Virus Particle

Section: 7 Contact Us

Subject: 7.1 Have Questions for Whole VIPERdb Team Members?
Subject: 7.2 Have Questions for Particular VIPERdb Team Member?
Subject: 7.3 Questions Regarding to This Site?

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 that exclusively deals with the high resolution virus structures determined using X-ray crystallography. All the unique virus structures at this site are organized in a standard orientation: Z(2)35X(2). Each virus structure (entry) is represented interms of its surface features, quasi-symmetry, capsomeric organization. Also each entry is analyzed interms of subunit-subunit contacts and association energies using the program CHARMM. In future details about the assembly intermediates & pathways and crystal contacts will be listed.

Subject: 0.2 The history of VIPERdb
This site was originally created and still being developed as the service/training and dissemination component of the NIH research resource: Multiscale Modeling Tools for the Structural Biology (MMTSB). The two groups at The Scripps Research Institute that are primarily involved in creating this site are:

1) Prof. Jack Johnson's group , who specializes in virus structure and function
2) Prof. Charles Brooks's group , who spear heads the computational aspects of the virus structures.

Subject: 0.3 About the FAQ
What kind of questions get into the faq?
Any that we think and find important! We will definitely include any questions that come us from the users of the VIPERdb site.

Who writes this?
This faq is written and maintained 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.

When will the faq be updated?
Revisions are made at least 3-4 times a year.


Section: 1 Navigation


Subject: 1.1 How to Navigate with the Menu at the Left?
Use the scroll bar on your browser to move throughout the page. To switch topics, you may click on one of the headings on the left frame (margin). The topics are as follows:

  • Overview: Provides a brief description about the VIPERdb.
  • Data: Virus data provided by viper, such as an alphabetical listing of the available virus structures, as well as a collection of various computational analysis that are being done on the virus structures.
  • Utilities: Tools provided by VIPERdb to allow the user to further explore virus particles.
  • Search: Allows you to find a Virus according to your specifications.
  • Help: Useful Help pages
  • Links: Provides links to useful sites and sites directly relavent to the VIPERdb.
  • Guestbook: A collection of entries from visitors to the site.

Subject: 1.2 How to navigate with the pull down VIPERdb Entry Menus?
There are two pull down menus, labeled 'CRYO-EM Entries', and 'X-RAY Entries', which list the viruses in our database. Left click on the pull down menus and select on the virus entry that you would like to visit. Selecting it should bring you to that page automatically.


Section: 2 Contents of VIPERdb


Subject: 2.1 Alphabetically ordered by the VIRUS names:
Virus names are ordered alphabetically and listed in the form of a table.

Subject: 2.2 Organization by the quasi and pseudo symmetry:
Lists of virus structures organized interms of their T numbers.

Subject: 2.3 Calculations:
Brief description of the various types of analysis that are being done or proposed on doing. Results of the some of the analysis can be seen by going to pages of the individual entries (click of the virus of choice) and follow the links under the section on "Computations".


Section: 3 Organization of Images


On each individual virus/entry page, you may find four images. You may click on each image to pull up the enlarged version of the image in a separate window.

Subject: 3.1 Rendered Surface:
Surface rendering of the virus particle (top left) generated using GRASP based on the atomic coordinates of the viral capsid proteins. The colors are depth cued with red at higher Z-coordinate(radius), white/gray at intermediate radius, and blue at lower radius. This rendering is designed to give an impression similar to that of a cryo electron miscroscopy reconstruction at 20 Å resolution. The redndered surface representations readily brings out large-scale features such as "canyons", "mountain tops" 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 fixed scale. Thus it is possible to create a gallery/montage of viruses that are scaled to each other by combining these images for various the viruses. A color bar has also been provided, which lists the values of the Z-coordinatecorresponding to the colors seen on the redered surface. These values can infact provide you the relative sizes of the viruses.

Subject: 3.2 Ribbon Drawing of the Subunits:
Ribbon drawing of the subunit(s) (lower left) 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, only one of the copies is shown. For picornavirus and related capsids there will be three ß-sandwich domains. The ribbon drawings are colored with tones changing continuously through the spectrum from blue at the N-terminus to red at the C-terminus. Strands of ß-sheets are depicted as arrows pointing in the direction of increasing sequence and helices are shown as coiled ribbons. Random coiled regions are depicted as tubes.

Subject: 3.3 Geometric Description of the Capsid:
Geometric description of the capsid (upper right) 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 Capsomeres Depicted as C-alpha Drawings of Subunits:
Capsomeres depicted as C-alpha drawings of subunits (bottom right) shows the detailed association of subunit C-alpha backbones to illustrate the dominant interactions within the particle. A portion of the geometric cage shown in the upper right is filled in with viral subunits to illustrate the relationship between chemistry and geometry that exists in these remarkable assemblies. Click on the image to be able to see an enlarged view

Section: 4 Using the information

Subject: 4.1 How to save the Coordinates, Images etc.,
At the top left corner of each of the individual virus pages are links to the header file, the transformation matrix, and the transformed PDB coordinates. 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. Please use your browser's back/forward options to get back to the entry page.

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 reorgnaized to suite the 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 How to Enlarge?
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 How to Compare Two or More Images? (valid for surface renderings only)
Visit the Visual VIPERdb 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 during crystallization.

Subject: 4.4 Where to Find Mutants and Related Entries for a Virus?
Mutant entries can be accessed from the entry for the wild type 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 you should see the links under Related Entries.

Subject: 4.5 How to Search the Contents of This Site?
You can search through our entire database of Virus entries using the Find a Virus page, in which you enter the traits of the viruses you're searching for. There are also 2 other site search methods:

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, complete virus capsid will be generated. Certain matrices from this list of sixty were used to generate capsomeres of the virus particle. Please note that these matrices correspond to particles in the standard orientation (See above)! 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 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 to the VIPERdb Team?
The email link is everywhere through out the site. You can click on any of them to send us your questions. The address is viper@scripps.edu.

Subject: 7.2 Have Questions for Particular VIPERdb Team Member?
Click here to the members' emailing list page.

Subject: 7.3 Questions Regarding to This Site?
This site was created and maintained by the VIPERdb Team. Questions regarding to the site should be addressed to reddyv@scripps.edu.





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