
Welcome to ProtDeform.

To install: execute ./install
To run:     execute perl StartProtDeform.pl  pdbfile1 pdbfile2 dirID 1

Output: see   dirID/README in the pymoldisplay_dirID.tar
        
This version is for linux, Intel x86.
For other platforms, you need new CLAPACK libraries and recompile. 

If you do not need the pymol display files then drop the last parameter "1" from the 
StartProtDeform.pl call.


Thanks for using ProtDeform.
REFERENCE:
J. Rocha; J. Segura; R. C. Wilson; S. Dasgupta : Flexible structural protein alignment by a sequence of local transformations. Bioinformatics, July, 2009; 25: 1625 - 1631.

Questions:

jairo.at.uib.es

ProtDeform Options

StartProtDeform.pl is a wrap of ProtDeform. If you plan to use ProtDeform a lot you should
know that ProtDeform needs proteins in the efficient bssp format, created by pdb2bssp.pl and bssp.pl files, and needed by the first classifier of Matras. 

The typical call of ProtDeform is

./ProtDeform P -A prot1.bssp -B prot2.bssp [-O -|N|P -ia filename]

-O -  Outputs only the scores in the format  protname1 protname2 Nalign PDscore rawScore
-O N  Normal output including alignment (default)
-O P  Normal output plus output for pymol display

-ia  filename  Reads the alignment and calculates only the score
               The format of the file is like
               
1 22
2 23
3 31
4 32
5 -1
6 -1
...
                where the first amino acid in the pdb has number 1, and so on.



The binary PDscore and the source SCO/ refer to a version that very efficiently calculates
the PDscore only.  It does not uses SSE information so it may differ from the full calcualtion
done by ProtDeform.
The input alignment is the identity alignment from the pdb numbering. 



