[modeller_usage] Using only partial information for the model

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