Hi all I've prepared an structural alignment of my 3 protein templates using MatchMaker/Match-Align tools. The question is: when I add my target sequence to the profile obtained in the step before, Does this procedure change my previous structural alignment?, or It just aligns the added sequence to my profile. The parameters that I used to add my target sequence are: Blosum-62, gap open, and gap extension penalties: 12 and 1 respectively. The second problem I have, its not related to chimera, but may be one of you can answer it. My target only has 29 % of identical residues with my templates, so Should I use a less stringent parameters to make my alignment? Any help would be appreciated. -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221