[modeller_usage] sequence alignment of pdb file with missing residues

[Andy Arvai <>]

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