Mauricio Carrillo Tripp wrote: > Is there a way to keep the original target's residue numbering in > the final model instead of having them sequentially numbered > starting at 1?
Sure, but it depends on what you're doing... Are you using automodel? If so, what is your alignment? Or are you building your model in some other fashion?
If you have a PDB file containing the original residue numbering, you could use res_num_from(). See http://salilab.org/modeller/9v5/manual/node176.html
Alternatively, you can write a little loop in Python to go through all the residues in your model and assign new residue numbers and/or chain IDs (each residue object has a 'num' member, which is the PDB-style residue number). This gives you much more flexibility.
If you're using automodel, these modifications could go in special_patches (in which case you'll also need to use your new residue numbers in any extra restraints you add) or in user_after_single_model.
> As an example, this is my target's sequence (NOTE: "-" are not > gaps, are missing/unknown residues):
If you're using automodel to build a model with intentionally missing regions, you need a chain break (/) rather than/as well as gaps for each region. Otherwise, there will be no break in the backbone, which is probably not what you want.
>>P1;1s58 > SEQUENCE:1s58.ali : 19 :A: 554 :A:::0.00:0.00
If this is really a sequence, all the fields after SEQUENCE: itself are ignored anyway, so it's best to leave them blank to avoid confusion. If this is actually a structure you should say structureX: rather than SEQUENCE: and name the PDB file containing the structure that matches your sequence (not an alignment file, as you appear to be doing).
Ben Webb, Modeller Caretaker