Modeller does not (automatically) assign chain identifiers to the model
chains when you have a multi-chain model. So the numbering in your
first example will not work because the chain identifiers do not exist.
The numbering in your second example is correct and should work even
when you have chain breaks. If you combine the alignment from your first
example with the numbering in your second example you should get what
you want.
Best,
Roberto
--
Roberto Sanchez, Assistant Professor
Structural Biology Program, Department of Physiology & Biophysics and
Institute for Computational Biomedicine, Mount Sinai School of Medicine
Box 1677, 1425 Madison Avenue, New York, NY 10029
phone +1 (212) 659 8648, fax +1 (212) 849 2456
http://physbio.mssm.edu/~sanchez/
Nicolas Le Novere wrote:
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