hi i just want to know if there is any script available in modeller that put in dashes (gap character) instead of missing residues when sequence is read from pdb. I am using following script:
from modeller import *# Get the sequence of the 1qg8 PDB file, and write to an alignment filecode = '1qg8'e = environ()m = model(e, file=code)aln = alignment(e)aln.append_model(m, align_codes=code)aln.write(file=code+'.seq')
it is giving me file without missing residues but i need to have dashes in place of missing residues
On 5/23/17 11:37 PM, AMARA JABEEN AMARA JABEEN wrote: > i just want to know if there is any script available in modeller that > put in dashes (gap character) instead of missing residues when sequence > is read from pdb.
No, not in Modeller - it doesn't care about residues that don't have coordinates, since these are of no use in modeling. I imagine you could parse the SEQRES records though (or even just guess based on gaps in residue numbering in ATOM records), depending on how reliable your PDBs are.
Ben Webb, Modeller Caretaker