GENTPL(1)

NAME

gentpl - generate a MIDAS template from a Protein Data Bank coordinate file

SYNOPSIS

gentpl -r residue [-i infile] [-c radiifile]

DESCRIPTION

Gentpl is a utility program for generating a MIDAS template from a Protein Data Bank coordinate file. Standard input is assumed unless otherwise specified. One file is produced: the ASCII instruction file, residue.ins, where ``residue'' is the residue name specified on the command line. These files are placed in the directory defined by the MODELS variable in the user's program environment (see ``Building and Modifying MIDAS Templates'' in Part III of the MidasPlus User's Manual).

-r residue

specifies the residue name. This name must correspond to the residue name as it appears in the Protein Data Bank input file.

-i infile

specifies an input file. The input must be in standard Brookhaven Protein Data Bank format. The file may contain data other than the coordinate data for the specified residue, but these extraneous records are ignored.

-c radiifile

specifies a file containing the radii of the atoms used to calculate the connectivity. If no file specified, the program uses as default /usr/local/midas/resource/connect.tpl. The format of the radii file is a series of records containing the atom name followed by the atom radius in angstroms. At least one space must appear between the atom name and the radius.

-v

indicates verbose mode and is useful for tracking down errors.

BUGS

The radii file must be ordered such that in the case of overlapping atom names, longest names appear before shorter ones. For example, if the file contains the radius for both B and BR, BR must appear before B in the file.

SEE ALSO

midas(1) Protein Data Bank File Record Formats

AUTHOR

Laurie Jarvis

UCSF Computer Graphics Laboratory