The NDB network query interface (Figure 1) provides a subset of the capabilities of the NDBQuery program on the World Wide Web. The menu of available query interfaces is shown in Figure 12. The first interface option provides the most robust access to the NDB. The second interface provides a selection query interface using a simple one page form containing some of the most popular database attributes. The third interface performs a structure selection query and creates a status report for the group of selected structures.
The control menu for the robust query interface is shown in Figure 13. The selection query and report creation facilities provided by this interface are similar to those provided by the NDBQuery program. This interface allows the user to navigate through the database and to identify the database attributes which will be constrained in the selection query or appear in an output report.
In building a selection query, database features of interest are chosen from the table and column menus shown in Figures (Figure 14)and (Figure 15). Conditions are placed on the selected features using the form shown in Figure 16. This form permits the specification of a target value for the condition and the type of comparison to be made (e.g. equal to, greater than, containing the string, etc.). Multiple conditions are applied using the logical operator (AND/OR) specified with each condition. The result of a selection query is a menu of output options similar to those shown in Figure 17. From this menu it possible to display/retrieve the coordinates for the asymmetric and biological units for the structure, view the NDB Atlas entry for the structure, or view the structure using the RASMOL viewer [4]. An example of output from a selection query is shown in Figure 18.
In addition to these output options, the interface can be used to build tabular reports for the subset of structures that are returned by the selection query. From the main interface menu shown in Figure 13, a user can enter the report generation section of the interface and select the database features that will populate an output report. Reports are generated by the interface and returned to the network browser in the form of HTML tables (Figure 19).
The second query interface provides a simple alternative to the menu driven selection query. The simple selection form interface is shown in Figure 20. This selection interface presents a subset of the NDB database attributes in a one page form. This selection interface produces the same menu of output options as are provided by the more complicated menu driven selection interface.
The status query selection form is shown in Figure 21. This interface permits a selection query on the restricted set of features: NDB structure identifier, author, citation title, and status code. These features are typically available for all structures throughout the data curation process. The result of the status query is a status report similar to that shown in Figure 22.
Figure 12:
The NDB top level query options page. From this menu three query options may be selected:
the full WWW NDB query interface, the quick form-based query interface, and the status
query Interface. A tutorial describing the use of these query interfaces may also
be selected.
Figure 13:
The main menu of options for the full NDB query interface. This menu coordinates
the structure selection queries and tabular report generation.
Figure 14:
The table selection menu provides a list of the table organized in categories according
to content. Clicking on a table name from this screen will produce the list of columns
in the selected table.
Figure 15:
The column selection menu provides a list of the columns in a selected table. Each column is
displayed with a description and a few examples.
Figure 16:
The condition form allows the user to place a constraint on the value of the column attribute.
In this form, the selection condition that the space group be 
is added
to the selection query.
This condition on the space group will be appended to the existing selection conditions on
the a cell constant which are displayed at the bottom of the form.
Figure 17:
This form displays the list of the structures which have been selected by the current
selection query. A list of options which can be selected from this form include:
the coordinates for the asymmetric unit in mmCIF, PDB and NDB formats, the
coordinates for the biological unit in PDB format, the full NDB format entry,
the structure of the biological unit viewed using a RASMOL viewer [4],
and the coordinates of the biological unit returned to the user with the chemical/x-pdb
mime type.
Figure 18:
Example display from a structure selection query for NDB structure AHJ043[5]
showing the coordinates in mmCIF format and the structure viewed using the RASMOL
viewer [4].
Figure 19:
An example report created from NDB report preparation interface following a structure
selection query. The selection query picked B-DNA structures in space group
with an a cell dimension in the range, 23.5 to 24.5 Å. This example report displays
the sequences and cell dimensions for the selected structures.
Figure 20:
An example illustrating the use of the NDB Quick Query Form to select B-DNA structures
determined by author Dickerson, which contains no modifications nor mismatched base pairs,
and were determined in space group with resolution better than 1.5 Å.
Figure 21:
An example illustrating the use of the NDB status query form to select structures
that in being processed at the NDB and are waiting for materials or approval from
authors.
Figure 22:
An abbreviated NDB status report showing the author and the structure descriptor for
NDB structures with status code WAIT. A variety of dates indicating the
mile-stones of data processing are available in the status report but are not shown in this
figure.