Hi Sergio, If I understand correctly, you used "Edit... Add Sequence" in Multalign Viewer to add another sequence to the alignment output by Match->Align. That does not change the 3D structural alignment (how the structures are matched), and it also does not change the multiple sequence alignment from Match->Align except that additional gap columns may be inserted between the columns that were already there. In other words, there may be places where the new sequence has a residue but the sequences in the original alignment all have a gap position. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mul...

I recommend saving the Match->Align result in a Chimera session and/or as an alignment file, so that you can easily try different parameters for adding the new sequence. It is not possible to tell from % ID what the best parameters are... unfortunately it is always case- dependent. I can only recommend trying a few different settings and using your knowledge of these proteins and your intuition to decide which result is the best. However, some rough guidelines are that you could try the BLOSUM matrix determined for more similar % IDs to your situation (e.g. BLOSUM-30), and if you want fewer columns inserted in your original alignment, increase the gap penalties. It may be that the new sequence has a loop where the others do not, however, and in that case gaps should be inserted. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Mar 18, 2009, at 5:32 AM, Sergio Garay wrote:

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.