[modeller_usage] sequence alignment of pdb file with missing residues

Hi,

I'm a new user to modeller and I would like to do a sequence alignment to a known structure which has gaps in the pdb file. The alignment works with align2d, however the sequence of the missing residues in the pdb file is not used. Ideally I would like to use the pdb file and the full sequence (including the residues which are missing in the pdb file). I know I can do an alignment of two sequences, but I'm wondering if it would be possible to get the best of both worlds - using sequence and structural information from the pdb file and also sequence information from the missing gaps. I've tried putting the entire sequence at the start of the pdb file with the SEQRES pdb keyword, but this seems to be ignored. Thanks for any help.

Andy