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PATCH and chains

dear users,

I model a multimeric protein, and I need to patch several disulfide bonds.

If I use an alignment like

TTTTTT/
TTTTTT/
TTTTTT/
TTTTTT/
TTTTTT*

MMMMMM/
MMMMMM/
MMMMMM/
MMMMMM/
MMMMMM*

SUBROUTINE ROUTINE = 'special_patches'
       PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '126:A' '140:A'
       PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '188:A' '189:A'
       PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '126:B' '140:B'
       PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '188:B' '189:B'
# ...
       RETURN
END_SUBROUTINE

(which is supposed to work according to the manual) Modeller complains that
the synthax '126:A' is not recognized and stops. I then have to fuse all 
the subunits and perform the following

TTTTTT
TTTTTT
TTTTTT
TTTTTT
TTTTTT*

MMMMMM
MMMMMM
MMMMMM
MMMMMM
MMMMMM

SUBROUTINE ROUTINE = 'special_patches'
       PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '126' '140'
       PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '188' '189'
       PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '332' '346'
       PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '394' '395'
# ...
       RETURN
END_SUBROUTINE

Of course at the end I have one huge protein and I have to cut it by hand,
not very convenient ...

Any idea ?

PS: Is it me or an alignment without a final blank line is not read?

--
Nicolas Le Novère                                 
Neurobiologie Moléculaire, Institut Pasteur, 75724 Paris cedex FRANCE
e-mail :                   http://www-alt.pasteur.fr/~lenov
tel : 33-(0)1-45-68-88-44                         fax : 33-(0)1-45-68-88-36