pdbopen (1) - Midas delegate for browsing and opening PDB entries

PDBOPEN(1)

NAME

pdbopen - Midas delegate for browsing and opening PDB entries

MIDAS COMMAND SYNTAX

Command: pdbopen [-directory dir] [-index file]

DESCRIPTION

Pdbopen is a MidasPlus delegate that presents an X/Motif user interface that allows users to browse through an index of the Protein Data Bank (PDB) coordinate entries, examine information associated with each entry, and open entries in MIDAS. Pdbopen may be invoked with the following flags:

-directory: Set the directory to use as the PDB repository. The default directory is /mol/pdb.

-index: Set the file to use as the PDB entry index. The default index file is found in index/entries.idx in the PDB repository directory.

Pdbopen reads the PDB index file and then displays two windows: an index browser and an entry inspector. Each PDB entry consists of several fields, including its PDB ID code, compound information, and ascession [sic] date. The browser lists short forms of PDB entries of interest while the inspector displays all the fields of a selected PDB entry.

The index browser consists of a text list, a menu bar, and two buttons. The text list consists of PDB entries, one per line, displayed in a scrollable region. At most one entry in the text list may be selected using the mouse, and additional information about that entry is displayed in the entry inspector. The menu bar has three entries: Sort, Show and Hide. The Sort menu will sort the entries displayed in the text list according to the chosen field; the Show and Hide menus will show and hide the chosen fields in the short form used to display entries in the text list. The Open button sends a command to MIDAS to open the selected entry. The PDB entries displayed in the text list may be pruned using the entry inspector (see below); the Display All button adds all entries from the index file back into the text list so that another search for ``interesting'' entries may be done.

The entry inspector consists of a number of text fields and several buttons. Each text field corresponding to a field in a PDB entry and, when an entry is selected in the index browser, displays the value of the field. The Open button sends a command to MIDAS to open the entry with displayed ID code. The Find, Undo and Clear buttons are used to prune entries from the text list in the index browser. The Find button searches through the list of entries in the text list and removes any whose fields do not match the values given in the inspector text fields. For the Resolution and Zero fields, the values are compared numerically; a relational operator may precede the numeric value ``<= 2'' means less than or equal to two) and a missing operator implies equality. For all other fields, the values are treated as case-independent regular expressions; a field is defined to match the value if any part of the field string matches the regular expression (see Regular Expression Examples below). The Undo button will undo the effect of the previous Find. Two Undo's in a row is the same as doing nothing. The Clear button will clear all the text fields. Because an empty value in a text field matches anything, Clear is useful if the subsequent Find only searches on one or two fields. The Help button brings up a window displaying these instructions.

REGULAR EXPRESSION EXAMPLES

Pdbopen uses case-independent egrep(1)-style regular expressions. The simplest regular expression is a string with no magic characters. For example, a value of ``serine'' will match the field ``HYDROLASE(SERINE PROTEINASE),'' because the field contains the string ``serine.'' Magic characters (i.e., ^$.*+()[]|\) are used to construct more complex regular expressions, such as ``[rd]na'' which will match all fields containing either the string ``rna'' or ``dna.'' Finally, the following expression matches A-T and T-A transitions (in the Compound field for DNA): ``[(CATGUP]AP*T[)CATGUP]|[(CATGUP]TP*A[)CATGUP].''

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