/usr/share/doc/garlic-doc/commands/cre.html

<html>

<head>
<title>
CRE, CREATE
</title>
</head>

<h1 align=center>

CRE, CREATE

</h1>

<hr size="3">

<font color=#880000>
<b>
NAME
<br>
</b>
</font>


CRE, CREATE - create structure
<br><br>


<font color=#880000>
<b>
SYNOPSIS
<br>
</b>
</font>


CRE
<br>
CREATE
<br><br>


<font color=#880000>
<b>
DESCRIPTION
<br>
</b>
</font>


Create structure, using the sequence from the main sequence buffer and the
secondary structure from the main secondary structure buffer. At present
(version 1.6), garlic is capable to create polypeptides only. Do not use
this command to create DNA or RNA structure.
<br><br>

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.
<br><br>

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.
<br><br>


<font color=#880000>
<b>
TEMPLATE RESIDUES
<br>
</b>
</font>


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):
<br>
(1) The current working directory.
<br>
(2) $HOME (user's home directory).
<br>
(3) $HOME/garlic (garlic subdirectory of the user's home directory).
<br>
(4) /usr/share/garlic (location for the system-wide file).
<br>
(5) /usr/local/lib/garlic (alternative location for the system-wide file).
<br>
(6) /usr/lib/garlic (another alternative location for the system-wide file).
<br><br>

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
very easy to add residues to the template file: just copy and paste the
chosen exotic residue from the PDB file where you have it to the end of
garlic template file. Be sure to include hydrogen atoms! There is one more
thing: be sure that your residue does not have the same residue serial number
as the preceding residue. You don't have to worry about the position and
the orientation of your residue.
<br><br>

If you don't have the file residues.pdb,
<a href="residues.html">
click here
</a>
for html version. It is very easy to convert this version to the plain PDB,
just save it as the plain text.
<br><br>


<font color=#880000>
<b>
EXAMPLE
<br>
</b>
</font>

<table border=2 cellspacing=2 cellpading=0>

<td align="left">

seq = asp ala phe tyr trp asn 
<br>
str = eeeeee
<br>
cre

</td>

<td align="left">

Define a short sequence (six residues),
<br>
use extended structure for all residues
<br>
and create the short peptide.

</td>

</table>

<br>

<font color=#880000>
<b>
NOTES
<br>
</b>
</font>


(1) The command CREATE resets the editing mode to default (no editing).
<br><br>


<font color=#880000>
<b>
RELATED COMMANDS
<br>
</b>
</font>

Use SEQUENCE to prepare the protein sequence and STRUCTURE to prepare the
secondary structure. The secondary structure buffer is initially filled
with MAXRESIDUES codes for extended structure (EEEEEEEE...).  MAXRESIDUES
is defined in the source file defines.h . BONDS REFRESH may be used to
fix bad bonds, which may sometimes be generated after executing the
command CREATE.
<br><br>


<hr size="3">

</html>
garlic-doc 1.6-1 / usr / share / doc / garlic-doc / commands / cre.html
