all new programs are in the jprotein folder


MakeInterface.java  

computes the complex interface
same option than JET -woi  (pdb and name of outputfile)
in exit it gives namepdb_inter_axs.pdb (annotated pdb with colors on the interface)

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TestMethods (only for comparing crystallographic complexes)

takes as input :

1. the annotated pdbfile (with JET/ET/IC methods)
The Consurf/ET file is transformed into JET formalism using TransformET and TransformCons

2. the complex interface file

3. output_filename

the output file has 5 columns:

- coverage percent
- surface coverage percent
- sensibility
- specificity
- surface specificity


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In JET we can now recover all trace levels (over all trees) doing 

JET options > trace_filename



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right now JET does not have the possibility to see intermediate trees.
soon Ladislas will change it.





 