Hello,
I am modelling a pentameric protein based on a template with missing residues, e.g. aaaaabbbbbdddddeeeee (except the original protein sequence has "ccccc" corresponding to a long disordered region between the "b" and "d", but this is not modelled, hence the FASTA of the protein looks like the above, and the .pdb file and 3D model of the protein would show "missing residues" between "b" and "d")
The original sequence of the target protein is: fffffggggghhhhhiiiiijjjjj except "iiiii" is a disordered region which aligns with "ccccc" in the template. If I remove "iiiii" from the sequence before aligning with the above template sequence (without the disordered region), "h" and "j" will be interpreted as continuous in the .pdb file of the target generated, affecting the structure of the protein. How would I make PDB interpret a gap between "h" and "j" that aligns with the gap between "b" and "d" in the template?
With thanks and kind regards, Amanda