Dear all, I am using MatchMaker for aligning about 100 structures, and it works very well!! Is it possible to automatically save the pairwise alignment without opening the MultAlignViewer? Due to the large number of structures, I cannot use the Match-Align tool but it would be enough to save the pairwise alignments Thanks in advance Tiziano -- +++++++++++++++++++++++++++++++++++++ Tiziano Tuccinardi, PhD Dip. Scienze Farmaceutiche Via Bonanno 6, 56126 PISA Tel ++39 050 2219595 Fax ++39 050 2219605 E-mail tuccinardi@farm.unipi.it <mailto:tuccinardi@farm.unipi.it> http://www.mmvsl.farm.unipi.it/staff/tiziano-tuccinardi/ Adjunct Assistant Professor SbarroInstitute for Cancer Research and Molecular Medicine Centerfor Biotechnology TempleUniversity PhiladelphiaPA 19122 (USA) +++++++++++++++++++++++++++++++++++++