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<html>

<head>
<title>
STR, STRUCTURE
</title>
</head>

<h1 align=center>
STR, STRUCTURE
</h1>

<hr size="3">

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

STR, STRUCTURE - manipulate the content of the secondary structure buffer.
<br><br>

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

STR = one_letter_code
<br>
STR LOAD filename
<br>
STR READ filename
<br>
STR FROM structure_identifier
<br>
STR COPY
<br>
STR SAVE filename
<br>
STR RESET
<br><br>

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

The command STR (long form: STRUCTURE) manipulates the content of the main
secondary structure buffer. Garlic mantains two secondary structure buffers:
the main buffer and the reference buffer. The main secondary structure buffer
is used to create a new structure and to replace a portion of an existing
structure.
<br><br>

By default, the entire main secondary structure buffer is initially filled
with codes for extended structure (i.e. filled with EEEEEEEE...). The number
of codes is set to MAXRESIDUES (defined in defines.h). This is done once,
when the program starts. When you change the content of this buffer, the
leading portion of the buffer will be filled with the last secondary
structure and the remainder will be filled with old codes. Use the command
STR RESET to reinitialize the buffer before using the command CREATE.
<br><br>

Both buffers store the following secondary structure information:
<br>
(1) The length of the secondary structure.
<br>
(2) The secondary structure (one letter codes). The codes are:
<br><br>

C = coil,
<br>
E = strand,
<br>
G = 3-10 helix,
<br>
H = alpha helix,
<br>
T = turn.
<br><br>

As the secondary structure information may be defined independently from any
structure, atomic coordinates are not required for most secondary structure
manipulation routines.
<br><br>

All versions of the command STR, except one, are used to manipulate the
content of the main secondary structure buffer. The only exception is
STR COPY, which copies the content of the main secondary structure buffer
to the reference buffer. This is the only way to initialize the reference
buffer.
<br><br>

<font color=#880000>
<b>
STR = one_letter_code
<br>
</b>
</font>

The command STR may be used with the keyword = (equal sign) to define the
secondary structure at garlic command prompt. This may be practical to define
the secondary structure of a short peptide or a small protein. The syntax:
<br><br>
STR = one_letter_code
<br><br>
Example:
<br><br>

str = ccccccchhhhhhhcttteeeeecccccccccccccc
<br><br>

The secondary structure will be converted to uppercase. If at least one
bad code is found, the command will fail and the main secondary structure
buffer will be left empty. Space, comma and tab may be used as separators.
<br><br>

<font color=#880000>
<b>
STR LOAD filename
<br>
</b>
</font>

The keyword LOAD (or READ, short forms LOA and REA) may be used to read
the secondary structure from the specified file. The input file should be
written in a format similar to FASTA. Empty lines and lines beginning
with # will be ignored. The number of codes per line is arbitrary. Example:
<br><br>
<img src="str.gif">
<br><br>

The following characters are threated as separators:
<br>
(1) space
<br>
(2) tab
<br>
(3) comma (,)
<br><br>

If input file contains at least one bad code (a residue name which consists
of four letters, for example) the reading will fail. The hard-coded maximal
number of residues is 20000, but it may be easily changed (see MAXRESIDUES
in the header file defines.h).
<br><br>
Example:
<br>
load secstr.fasta
<br><br>

<font color=#880000>
<b>
STR FROM structure_identifier
<br>
</b>
</font>

The keyword FROM (short form: FRO) may be used to copy the secondary
structure from the specified atomic structure to the main secondary
structure buffer. Only the structure of selected residues is copied.
Residue is treated as selected if the first atom is selected. For proteins,
this is typically N (nitrogen).
<br><br>
Example:
<br>
str from 1
<br><br>

<font color=#880000>
<b>
STR COPY
<br>
</b>
</font>

The command STR COPY (short form: STR COP) copies the secondary structure
from the main secondary structure buffer to the reference buffer. This is
the only way to initialize the reference buffer. This command must be
executed (i.e., the keyword COPY must be used) before executing commands
which require two secondary structures for proper operation. The main
secondary structure buffer may be initialized prior to STR COPY by using
one of the keywords described above (=, LOAD or FROM).
<br><br>
Example:
<br>
str copy
<br><br>

<font color=#880000>
<b>
STR SAVE filename
<br>
</b>
</font>

The command STR SAVE (short form: STR SAV) saves the secondary structure
to the specified file. The output file will be written in FASTA format.
<br><br>
Example:
<br>
str save 9pap.secstr
<br><br>

<font color=#880000>
<b>
STR RESET
<br>
</b>
</font>

Reset (initialize) the main secondary structure buffer. The short form
is STR RES. The command STR RESET sets the number of codes in the main
secondary structure buffer to MAXRESIDUES (defined in defines.h) and
fills the entire buffer with codes for extended structure (EEEEEEEE...).
<br><br>

Example:
<br>
str reset
<br><br>

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

SEQ may be used to define the sequence. CREATE may be used to create a new
peptide.
<br><br>

<hr size="3">

</html>