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DESCRIBE -- describe proteins

ATOM_FILES = <string:0> '' complete or partial atom filenames
ATOM_FILES_DIRECTORY = <string:1> './' input atom files directory list (e.g., 'dir1:dir2:dir3:./:/')
ALIGN_CODES = <string:0> 'all' codes of proteins in the alignment

Requirements:
[alignment]

Description:
This command outputs basic data about the proteins whose atom filenames are specified by ATOM_FILES or ALIGN_CODES. An alternative specification of the proteins to be described can be provided by the alignment in memory; i.e., READ_ALIGNMENT followed by DESCRIBE will describe all the proteins in the alignment. This command is useful for preparation before comparative modeling because it summarizes disulfides, cis-prolines, charges, chain breaks, etc. When an alignment is given, results depending only on the amino acid sequences are still written out even if some atom files do not exist.

Example:


# Example for: DESCRIBE

# Describe the sequences and structures in the alignment.

READ_ALIGNMENT FILE = 'toxin.ali', ALIGN_CODES = '2ctx' '2abx'
DESCRIBE


next up previous contents index
Next: ID_TABLE calculate Up: Comparison and searching of Previous: EDIT_ALIGNMENT edit   Contents   Index
Ben Webb 2004-10-04