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