Dan, you need to use the SEQUENCE_TO_ALI command first, to copy the models' sequences and coordinates into the memory. Check the manual for explanation and example under sequence_to_ali ( and compare_alignments). The fact, that you have identical sequences in your models, should not have any effect on the structural alignment. Andras Dan Thomas Major wrote: > > I'm trying to align the structures that modeller produces by using the > following top script: > > SET ATOM_FILES = 'hp2y1.B99990001' 'hp2y1.B99990002' 'hp2y1.B99990003' ; > 'hp2y1.B99990004' 'hp2y1.B99990005' > SET WRITE_FIT = on > SET MAXRES = 2000 > MALIGN3D > > Modeller gives an error: > malign3_327W> Only one structure; nothing done. > > How can I tell modeller to align the structures even if they are the same? > Thanks, Dan > > -- > Dan Thomas Major (at Dr. B. Fischer's lab) > Bar-Ilan University > Ramat-Gan, Israel > > -- , Andras Fiser, PhD # phone: (212) 327 7216 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras