CRE, CREATE
NAME
CRE, CREATE - create structure
SYNOPSIS
CRE
CREATE
DESCRIPTION
Create structure, using the sequence from the main sequence buffer and the
secondary structure from the main secondary structure buffer. At present
(version 1.4), garlic is capable to create polypeptides only. Do not use
this command to create DNA or RNA structure.
Both buffers have to be initialized before issuing the command CREATE. A
typical use will be to create a short peptide, which will be tryed as an
inhibitor for a larger, experimentally determined structure.
The present version (garlic 2.1) will correctly interpret the secondary
structure codes for alpha helix (H), 3-10 helix (G) and beta strand (E),
while coil (C) and turn (T) will be treated the same way as beta strand.
TEMPLATE RESIDUES
The new structure will be created using the residues from the template file.
The template file contains 20 standard residues. This file should be named
residues.pdb and stored to at least one of the following directories
(listed in the search order):
(1) The current working directory.
(2) $HOME/garlic (garlic subdirectory of user's home directory).
(3) /usr/local/lib/garlic (the system-wide template).
If you want to add some extra residues (like modified amino-acids) to the
template file, make your own copy of the file residues.pdb and keep it either
in $HOME/garlic subdirectory or in your favorite working directory. It is
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