[modeller_usage] handling missing residues in pdb files when doing multiple alignments

[Mike White <>]

I am modeling a homopentamer in several different conformations using
multiple templates as described in the Advanced tutorial. My modelling
process involves using three different templates from homologous
proteins and getting a structure-based alignment of the templates using
salign. One of the templates has several gaps in the same position in
each of the subunits (missing 1-3 amino acids in the structure).The
resulting structure-based alignment doesn't show the missing residues as
gaps of the proper length (this may be because the missing residues are
in the middle of long loop without structure at subunit-subunit
interfaces and one might be able to do without one or two residues
here).

I know that when one uses a single template with missing residues one
should correct the alignment between the sequence to be modeled and the
template by introducing gaps in the alignment for the missing residues.
At what point would one deal with this when using multiple templates? If
you insert the gaps in the structure-based alignment before aligning the
sequence, are the gaps preserved, or do you then have to tweak the final
alignment a bit more before modeling?

I assume that the "adjustments are made in the 

Thanks

Mike White