first of all I'd like to thank you for helping with my last question.
Now I have another question. I have to build a model by homology modelling for a protein(only sequence available) which builds a homodimer. The template-structure is a homodimer as well. I used the following script to align the sequence and the structure.
from modeller import *
env = environ() aln = alignment(env) mdl = model(env, file='y', model_segment=('FIRST:A','LAST:B')) aln.append_model(mdl, align_codes='y', atom_files='y.pdb') aln.append(file='x.ali', align_codes='x') aln.align2d() aln.write(file='xy.ali', alignment_format='PIR') aln.write(file='xy.pap', alignment_format='PAP')
In the resulting alignment there is a separation ("/") between the two chains of the template sequence. But in the sequence of the target there isn't a separation of course. Do i have to put a separation in the sequence of the target in the alignment file or in the input file for the alignment script? Or whats the best way to handle this problem ? If I put the separation in the resulting alignment the alignment of the chains wouldn't be good. Does the x.ali file of my target have to look like this:
>P1:x .... XXXX / XXXX
Is it sufficient to use the following script afterwards to build the model out of the alignment ?
from modeller import * from modeller.automodel import *
env = environ() a = automodel(env, alnfile='xy.ali', knowns='y', sequence='x', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 5 a.make()
Thank you very much
Christopher Mohr wrote: > In the resulting alignment there is a separation ("/") between the two > chains of the template sequence. But in the sequence of the target there > isn't a separation of course. Do i have to put a separation in the > sequence of the target in the alignment file or in the input file for > the alignment script? Or whats the best way to handle this problem ?
I don't think I quite understand your question, but the usage of chain breaks ("/") in your alignment is simple - if you have a chain break in the target sequence, Modeller will not link the backbone between the residues either side of the break. If this is what you want, put in a chain break, and if not, don't.
Since a chain break is not a "real" residue, you should always align it with another chain break, or a gap, in the template structure(s).
Ben Webb, Modeller Caretaker