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I have tried in vain to get model_loop to work properly using either 
modeller6v1 (directly using the model_loop script in
or  modeller6v0 (when asking for modelling two loops at once).
The modelled structures are 'blasted up' with numerous atoms far away
the core structure. However, asking for modelling one loop at once
using modeller6v0 is find.

The option SET DO_LOOP in __model.top is failling similarly.

A slight detail PDB_EXT is applied to both sequence.BL00..., 
sequence.DL00... and sequence.IL00... files

That's too bad as the new loop procedure looks promising.



Dr Gilles Labesse 
Centre de Biochimie Structurale		Tel : +33 (0)4 67 04 38 47
INSERM U554 - CNRS UMR5048 - UM1	Fax : +33 (0)4 67 52 96 23
15, Av. Charles Flahault		
34060 MONTPELLIER Cedex - FRANCE   http://www.cbs.cnrs.fr/~labesse/