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**                                                            **
**   PDB Raider 1.1 --- version Linux (August 2004)           **
**   EBGM (Equipe de Bioinformatique Genomique et Moleculaire **
**   E 03 46 INSERM - Universite PARIS 7                      **
**   2, place Jussieu, case 7113                              **
**   75251 PARIS Cedex 05 - FRANCE                            **
**                                                            **
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This program has been done to work with PDB file. It's main purpose
was to code the protein in terms of Protein Blocks (de Brevern et al., 
Proteins, 2000). Since  numerous other things have been done but are 
not explain (in fact, it is in french). This software has been used
to parse different secondary structure assignment and allows to
create simple databank in flat file format (like the one I use for
de Brevern et al., Protein Science, 2002 and de Brevern & Hazout, 2003,
Fourrier et al., 2004;
look at : http://www.ebgm.jussieu.fr/~debrevern/DOWN/DB/index.html).

You can find here a "minimal" help to code the proteins in terms
of Protein Blocks. For other purpose, please ask me.
This software is distributed in the hope that it will be useful, 
but WITHOUT ANY WARRANTY.

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INSTALLATION GUIDE :
--------------------

# 1 - create a subdirectory {exemple Lect)
#-----------------------------------------

mkdir Lect

# 2 - go to this subdirectory
#---------------------------
cd Lect

# 3 - put the archive in this subdirectory
#-----------------------------------------

mv ~/???/lecture.tar.gz .

# 4 - uncompress the archive
#---------------------------

tar xzvf lecture.tar.gz 

# 5 - create another subdirectory [not in the archive]
#-----------------------------------------------------

mkdir Db

# 6 - compilation
#----------------

make

# 7a - clean
#-----------

make clean

# 7b - clean
#-----------

rm -rf lecture.tar.gz 

# 8 - test
#---------

{syntaxe} lect -Fichier_PDB [pdb_file] -No_Check -PBs  

lect -Fichier_PDB Special/2AAK.pdb -No_Check -PBs  

{after look in the Results/} Results/fasta_block.txt

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{its the "regular" result :}

>2AAKA    151 BP16  2.4
ZZfklmmmmmmmmmmmmmgcehiacdddfklckbccddddd
dehifkgoiacdddddddfkbckbccddddfbdcddfklcf
kopacdfklmmmpcfklcfklmmmmmmmmmmopcfklpfbl
mlmmmmmmmmmlmmmmmmmmmmmmmZZ
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B- some examples of the PDB Raider use :

(1) For a short summary of PDB files :
--------------------------------------

lect -Fichier_PDB  temp/1AP9.pdb -No_Check -PBs -DbT

The resulting file is : Results/Rasta/1AP9.rsy [see CODE/DATA/EX/]

if DSSP, STRIDE, ... are well installed, you can do :

lect -Fichier_PDB  temp/1AT9.pdb -No_Check -PBs -DbT -Dssp  -Stride -Writedef -Psea -Define -Vcurve -helanal -xtlsstr -RKstr -Fodje

The resulting file is : Results/Rasta/1AT9.rsy [see CODE/DATA/EX/]




(2) For the creation of a simple databank (http://www.ebgm.jussieu.fr/~debrevern/DOWN/DB/index.html):
-----------------------------------------

lect -Fichier_PDB  temp/1AT9.pdb -No_Check -PBs  -DbkPN -Writedef -DbName one_prot

The resulting file are : Results/one_prot et Results/expl_one_prot [see CODE/DATA/EX/]



(3) For the generation of Molscript files (with different secondary structure assignments):
-------------------------------------------------------------------------------------------

(need Raster3D)

 lect -Fichier_PDB  temp/$ligne -No_Check -PBs [S2 -Dssp] -Molscript 
 
=> It will generate a file in Results/Rasmol/ 
  
 lect -Fichier_PDB  temp/$ligne -No_Check -PBs [S2 -Dssp] -Molscript  -MolVideo

=> It will generate 360 files (molscript alone) in Results/Rasmol/ [a_molscript_DSSP_rotate_1AP9_0_0_for.43.000000.jpg]
		and 360 files (w/ Raster3D) in Results/XYZ/ [molscript_DSSP_rotate_1AP9_0_0_for.43.000000.jpg]

	The file Results/Rasmol/rotate_molscript3.scr use convert to create the mpeg movies.
	
     cp Results/Rasmol/rotate_molscript3.scr Results/XYZ/
     
     cd Results/XYZ/
     
     chmod u+x rotate_molscript3.scr
     
     ./rotate_molscript3.scr
     
=> It will create mpeg files like :      
     
  However sometimes, we need to change the axes of the PDB files, so please use :
  
  ......   
	
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For more details contact me at :Alexandre.deBrevern@ebgm.jussieu.fr

		Alexandre de Brevern 	     [v1.1 - 02-AUG-2004]

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EBGM    Alexandre G. de Brevern                              EBGM
EBGM    Equipe de Bioinformatique Génomique et Moléculaire   EBGM
EBGM    INSERM, E03-46, Université Paris 7, case 7113,       EBGM
EBGM    2, place Jussieu, 75251 Paris Cedex 05 - FRANCE      EBGM
EBGM    mail: Alexandre.deBrevern@ebgm.jussieu.fr            EBGM
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