[modeller_usage] Using only partial information for the model

[Stéphane Téletchéa <stephane.teletchea@jouy.inra.fr>]

Dear colleagues,

I'm willing to use modeller in a specific modelling procedure where only 
specific parts of the model are wanted.
In fact, i have two beta sheets and two helices in the pdb template, and 
there are linked via loops.
I would like to know the procedure i need to follow in order to model 
only those subparts of the system (and use modloop for the linking part).
For instance this will be for the alignment:
>template;
structureX:18:A 63:A :::
XYZXYZ-----AAAAALLL----BBBBBLLL---AAAAALLLLL--BBBBBLLL-------*
>target;
sequence:1:::::
------CCCCCAAAAA---CCCCBBBBB---CCCAAAAA-----CCBBBBB---CCCCCCC*

The matching sections are 'A' (alpha) and 'B' (beta), other letters 
being for illustration.
The template pdb contains all the coordinates for the important 
structures, but not for loop LLLLL (third one).
Do i need to adjust the alignment or the python script (or both)?
I've searched through the archives and tutorials without clue, i'm 
probably not getting all the process properly.
Thanks a lot in advance,

Stéphane

--
Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901