About this Atlas
The NDB Atlas of Nucleic Acid Structures was developed to highlight the special
aspects of each structure in the NDB.

How were the Atlas pages generated?
Each page is generated directly from NDB using an XML translator which formats the data contained in each NDB file. Pictures present on the Atlas pages were generated by different software. Blocview (a graphics program developed by Xiang-Jun Lu) was used to generate pictures of the asymmetric units and biological units for x-ray structures and was used to generate the representative model pictures for NMR structures. RNAview (a graphics program developed by Huanwang Yang in collaboration with Fabrice Jossinet and Eric Westhof) was used to generate two-dimensional represenations of RNA structures. MaxIT (Macromolecular Exchange Input Tool developed by Zukang Feng and John Westbrook) was used to generate crystal packing pictures for x-ray structures and ensemble pictures for NMR structures.

The Atlas has evolved into its present form due to the participation of several groups of students. The original version of the Atlas was created by the following students: Lindsey Lair, Kavin Mistry, Ketan Patel, Audrey Swamy, Judy Tsai, and Julie Woda. The second version of the Atlas was part of an NDB Summer Program, with Sam Engel, Mike Mehnert, Ketan Patel, Ivan Sirett, and Maria Steffero participating. Additional developments on the Atlas were then made by Debra West and Sesh Venugopal. The current version of the Atlas is a result of the NDB Summer 2002 program, with Goran Aleksic, Joanna de la Cruz, Gregory Donahue, Dipannita Kalyani, Dan Kulp, and Hari Narayan participating.

How are the images colored?
In the nucleotide block models, adenine is red, thymine is blue, cytosine is yellow, guanine is green, and uracil is cyan. In the atom stick models, carbon is black, oxygen is red, nitrogen is blue, and phosphates are orange.

How are modifications in the sequence shown?
In the sequence section of an atlas page, modified bases are designated with the modifier following the base. A modifier designated after the p in the compound name indicates that the sugar phosphate is modified.

How is the Atlas organized?
The Atlas is first divided by how the structures were determined: by X-ray crystallographic or NMR experiments. Gallery index pages, which include images for each structure on the page, and plain text index pages, are offered.

These index pages are then divided into several categories that were created by using a variety of constraint parameters, such as conformation type or presence of modifications, drugs, etc. Several structures appear in multiple categories.

How are the Atlas pages used?
The Atlas pages serve many purposes. They are an invaluable aide in checking the structures contained within the NDB. They serve as a teaching tool for the many students who have created and checked the Atlas pages. Test versions of the Atlas have been very effective in teaching students at all levels about nucleic acid structure.

How can these Atlas pages be accessed?
These pages are accessible from the Atlas section of the NDB WWW site and as an output option from the NDB WWW Interface.