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 : lenov@pasteur.fr http://www-alt.pasteur.fr/~lenov tel : 33-(0)1-45-68-88-44 fax : 33-(0)1-45-68-88-36