readme.scwrl3

蛋白质中氨基酸名称的转换,将三字母的氨基酸转换成单字母

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                 SCWRL3.0 README 
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This file describes the installation procedure and provides a quick
reference guide for

SCWRL3.0 copyright (c) 2003 Adrian A. Canutescu and Roland L. Dunbrack Jr.
Fox Chase Cancer Center
Philadelphia, PA, USA

and it was created on July 1, 2003.

CONTACTS
========
Questions or problems about installation or use, please contact the authors:

Adrian Canutescu  [e-mail]
Roland Dunbrack   [e-mail]

INSTALLATION
============

SCWRL3.0 is provided in binary form for the following operating systems:
- Windows 9x/Me/2000/XP
- Linux
- MacOS X

and the installation kits for each operating system have the following
names, respectively:

- scwrl3_win.zip
- scwrl3_lin.tar.gz
- scwrl3_mac.tar.gz

After you download the installation kit appropriate for your operating
system, you should create a directory and uncompress it:

- for Windows, you have to use WinZip
- for Linux / MacOS X you have to:
      1.) gzip -d scwrl3_lin.tar.gz or gzip -d scwrl3_mac.tar.gz
      2.) tar -xf scwrl3_lin.tar or tar -xf scwrl3_mac.tar

The previous step will generate 4 files:
- BBDep.bin
- setup (setup.exe for Windows)
- scwrl3_
- README (this file)

The final installation step is to run setup (setup.exe for Windows)
from the directory in which you uncompressed the kit. 
Simply type

   ./setup

to the Linux shell or MacOS X terminal window, or

    setup.exe

to the command window for Windows.

Running setup will generate an executable file "scwrl3" ("scwrl3.exe"
for Windows) and will also hardcode the path toward the backbone-
dependent rotamer library (BBDep.bin). After this, you can move the
scwrl3 executable to a different location, or create symbolic links or
aliases for it, provided that you keep the backbone-dependent rotamer
library in the directory where you performed the installation. If you
decide to move the backbone-dependent rotamer library to a different
location, you have to repeat the installation procedure for that
director, beginning with uncompressing the kit.

QUICK REFERENCE
===============

Usage: scwrl3 -i <input_file> -o <output_file>  > logfile

Options:
-u disables the disulfide bonds identification
-s <sequence_file> loads a sequence file
-f <frame_file> loads a frame file
-d prints dihedral angles to a file called <output_file.dihed>

-i <input_file> [required]
The main input file to scwrl should be a protein backbone, with or
without sidechains, cofactors, or solvent. Residues with incomplete
backbones are treated as glycines. Residues with names that do not
match the standard 20 amino acid names are also treated as
glycines. The sequence of residues is read from the first atom in each
residue.  If you wish to change this sequence, the -s flag allows you
to enter a new sequence independently.

-o <output_file> [required]
The output file contains the identical backbone as the input file,
with predicted coordinates for the sidechains.

-f <frame_file> [optional] 
This file is used to add additional steric boundaries to the
sidechains. It should be in pdb format, and might contain cofactors or
metal atoms, lipid molecules, or another protein.  In any case, it is
held fixed and used only for steric clash checks.Radii were determined
from atom-atom distances in the PDB.  All elements currently observed
in the PDB can be treated by scwrl.

-s <sequence_file> [optional]

This flag is followed by a sequence file.  The sequence should have
the same number of residues in it as the input backbone. White space,
carriage returns, and numbers are ignored. Lower-case letters in the
sequence indicate that the Cartesian coordinates for the corresponding
residues are to be left untouched, and will be treated as steric
boundaries only for the other side chains.

Examples:
SDERYCNM - full SCWRL side-chain replacement
SdERYCNM - input residue (aspartate) is left where as is.
SxERYCNM - input residue (aspartate) is left where as is.

-u [optional]
Disulfides will not be calculated

-d [optional]
Specifies dihedral angles to be printed to a file <output_file.dihed>