ac_prediction 1.1
-----------------

The program was written by Oleg Sobolev.
Author will appreciate any questions, comments and 
bug reports to: sobolev@impb.psn.ru

PURPOSE: 
Ac_prediction makes prediction which side chains should be 
checked first with electron density maps because they are 
primary candidates to have alternative conformations.
The prediction is based on atomic shifts during unrestrained 
refinement. (3 macro-cycles of phenix.refine or 10 cycles of
Refmac).

REQUIREMENTS:
-------------
This program requires Python 2.6 or newer (not Python 3.x).
If you have python installed on your computer you can use it.
Otherwise you can try python from PHENIX package
(command: phenix.python).
See below some tips about installation on different operating
systems.

USAGE:
------
Mandatory arguments: two .pdb files.

Optional keys:
-o<output file name>	-Output filename
-r<Rfactor>		-Rwork of the model before unrestrained refinement
-s<resolution>		-Resolution of X-ray data
--refmac		-The refinement was run by Refmac
-t			-Use threshold-based criterion (Default)
-l			-Use likelyhood-based criterion
-n			-Sort output list by residue number

Example (with local python installation)
python ac_prediction.py 1hg7_1.pdb 1hg7_2.pdb
python ac_prediction.py 1hg7_1.pdb 1hg7_2.pdb --refmac -o1hg7.log -r0.12 -s1.15

The program will produce 1 text file file with results.


Also it is possible to use file with parameters:
python ac_prediction.py params.txt

===================params.txt begins========================
[main]
pdb1=1hg7_1.pdb
pdb2=1hg7_2.pdb
log_name=1hg7.log
refmac_refinement=False
threshold=True
resolution=1.15
rfactor=0.12
sort_residue_number=False
===================params.txt ends==========================

REFERENCE:
---------

1. O. V. Sobolev and V. Y. Lunin "Detection of alternative 
conformations by unrestrained refinement". Acta Cryst. D68.1118-1127.
2. O.V. Sobolev. DETAC: tools to detect alternative conformations 
by unrestrained refinement. (2012). 
Computational Crystallography Newsletter. 3.

REMARKS:
--------

======================Installation==========================

WINDOWS:
You can download windows installers of the necessary programs.
Python:		http://python.org/download/

To find out what version of Python you have installed type
"python" in command promt (cmd):

c:\>python
Python 2.6.6 (r266:84297, Aug 24 2010, 18:46:32) [MSC v.1500 32 bit (Intel)] on
win32
Type "help", "copyright", "credits" or "license" for more information.
>>>

If you have just installed python and version number in cmd window 
does not match version you have installed, examine system variable
PATH and make sure that path to your python installation is
situated in the beginning of it.

LINUX:
All necessary programs are packaged for almost every major 
Linux distribution. So if you are on Linux, your package manager 
will probably provide Python.

To find out what version of Python you have installed 
type "python":

oleg@ant:~$ python
Python 2.7.3rc2 (default, Apr 22 2012, 22:30:17)
[GCC 4.6.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>>

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