Hi Anna, My first impression is that MatchMaker is not the appropriate tool for such a study. You may instead wish to use one of the many "3D motif"-related software tools. There may be dozens of such resources, but to name a few: LabelHash server <http://labelhash.kavrakilab.org/> PINTS server <http://www.russelllab.org/cgi-bin/tools/pints.pl> funClust server <http://pdbfun.uniroma2.it/funclust/index2.py> pdbFun server <http://pdbfun.uniroma2.it/> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 6, 2014, at 2:59 AM, Anna Hernandez <annahernandezduran@gmail.com> wrote:

Hi,

I have a question regarding structural alignments with Match Maker. I would like to know if there is any way to obtain a list of all possible alignment solutions (or a subset) tested by Match Maker, instead of only the "best" one, so that I can further assess the different options manually.

Specifically I am trying to find an homologous substructure/motif from my template structure within a query structure. The pattern to be searched is rather small as compared to the whole protein and it can be aligned in multiple positions. I would like to assess each of the possibilities more carefully based on the biological knowledge of the protein.

Thank you in advance.

Best wishes,

Anna Hernandez