Taking into account additional residues
Hi all, my problem is the following:
I want to model a structure based on another one. Both are trimers. My sequence (corresponding to the "unknown" proteins) has additional residues at the beginning of each chain, and I have to force them to make an alpha-helix. The problem is that when I try to add the restraints using as template the original chains-including PDB file and separating chains in the .ali file, the residues numbering seems to start from the residue 1 of the template, and I can't impose anything on my sequence. I've tried too to edit the template PDB file in order to delete the information about chains and to obtain a "normal" numbering, but in this case, obviously, Modeller is not able to separate the subunits and generates strange distortions to keep in contact the boundary residues. Last possibility would be to model separately the chains and to reconstruct the trimer at the end, but the modeling changes the coordinates and I can not imagine how to reassemble the single results. Any suggestion?
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valeria losasso wrote: > I want to model a structure based on another one. Both are trimers. My > sequence (corresponding to the "unknown" proteins) has additional > residues at the beginning of each chain, and I have to force them to > make an alpha-helix. The problem is that when I try to add the > restraints using as template the original chains-including PDB file and > separating chains in the .ali file, the residues numbering seems to > start from the residue 1 of the template, and I can't impose anything on > my sequence.
I'm not sure if I fully understand your problem, but Modeller always numbers the *model* residues starting from 1 - the template numbering is ignored completely. This is, of course, so that it IS possible to add restraints on parts of the sequence which aren't in the template, as in your case. I suggest that you first build a model with no additional restraints, and then look at the output PDB (or if you are impatient, look at the unoptimized model - the .ini file - instead). You should be able to see the residue numbers and chain IDs of the model then, and use these in order to add your restraints.
Modeller should have no difficulty in building multi-chain models. Just add a / chain break character between each chain in the model sequence.
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
valeria losasso