# STR, STRUCTURE

NAME
STR, STRUCTURE - manipulate the content of the secondary structure buffer.
SYNOPSIS
STR = one_letter_code
STR LOAD filename
STR READ filename
STR FROM structure_identifier
STR COPY
STR SAVE filename
STR RESET
DESCRIPTION
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.
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.
Both buffers store the following secondary structure information:
(1) The length of the secondary structure.
(2) The secondary structure (one letter codes). The codes are:
C = coil,
E = strand,
G = 3-10 helix,
H = alpha helix,
T = turn.
As the secondary structure information may be defined independently from any structure, atomic coordinates are not required for most secondary structure manipulation routines.
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.
STR = one_letter_code
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:
STR = one_letter_code
Example:
str = ccccccchhhhhhhcttteeeeecccccccccccccc
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.
STR LOAD filename
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:
The following characters are threated as separators:
(1) space
(2) tab
(3) comma (,)
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).
Example:
load secstr.fasta
STR FROM structure_identifier
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).
Example:
str from 1
STR COPY
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).
Example:
str copy
STR SAVE filename
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.
Example:
str save 9pap.secstr
STR RESET
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...).
Example:
str reset
RELATED COMMANDS
SEQ may be used to define the sequence. CREATE may be used to create a new peptide.