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
Dear Nicolas, 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 > 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 > > > > > >
participants (2)
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Nicolas Le Novere -
Roberto Sanchez