EDPDB is a program to handle PDB (Brookhaven Protein Databank) format coordinate file(s). With EDPDB, a PDB file may work as a small database, where information like distances, angles etc. within the file can be easily obtained.
EDPDB is a command driven program. Each function in EDPDB is activated by a one-line input statement (a command or an input card). An input card starts with a keyword (ie. the name of the function) and includes parameters that may be required by the function. The leading keyword can be abbreviated as long as there is no ambiguity with other leading keywords. For example, command RESET may be abbreviated as RESE, but can not be abbreviated further (eg. RES) because of the existing command RESIDUE. The input parameters are separated from each other by function. The leading keyword can be abbreviated as long as there is no ambiguity with other leading keywords. For example, command RESET may be abbreviated as RESE, but can not be abbreviated further (eg. RES) because of the existing command RESIDUE. The input parameters are separated from each other by spaces or a comma (not a space followed by a comma). At the position where a parameter is expect, a comma may call the default value for that parameter if it exists. In most cases the order of the input parameters is organized so that required parameters are input first and optional ones later. Once an input card is entered the function is called immediately. For example, by typing ANALYZE, the average, minimum, maximum, range, and standard deviation of the x,y,z "coordinates", occupancy and B-factors of the current ON atoms will be listed. The order of the input cards, therefore, will determine the behavior of EDPDB.
Throughout this help documentation, in the syntax line a (...) means a list of parameters from which usually only one is needed, whereas [...] indicates that the parameters are optional.
By default, all the characters in an input statement will be converted to lower case before being interpreted, unless the environmental parameter tolower is set to off.
In an input statement, the text string within a pair of single quotation marks (ie. ' ') may be considered as a single parameter.
For more information on the general command syntax, see the command interpretation section in the glossary category, and a separate documentation titled as EDPDB: A Multi-Functional Tool for Protein Structure Analysis. (Zhang & Matthews (1995). J. Appl. Cryst.).
To report bugs, please contact
Cai X.-J. Zhang, at (cai-zhang@omrf.ouhsc.edu)Other programs available from the author: