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I ended up using multiprot and staccato recently http://bioinfo3d.cs.tau.ac.il/MultiProt/ There is a server for multiprot, but I downloaded the applications. I still ended up doing quite a bit manual editing in filling the gaps in the structures etc. I stumbled also over a link about the matter comparing different programs (by Dr Elaine Meng): http://www.cgl.ucsf.edu/home/meng/grpmt/structalign-content.html ~L~ ______________________________________________________ Lari Lehtiö Pharmacy, Department of Biochemistry and Pharmacy Åbo Akademi University, BioCity, FIN-20520 Turku Finland +358 2 215 4270 http://www.users.abo.fi/llehtio/ ______________________________________________________ Quoting Ronnie Berntsson <[log in to unmask]>: > Dear all, > > A bit off the topic question perhaps. > I am trying to find a program which can do multiple structural > sequence alignments. What I would like is a program which can take > as input PDB codes (or files), and which will output a multiple > sequence alignment in FASTA format with the full sequences of the > supplied proteins intact. Preferably said server/program should be > able to handle at least 20 input pdbs at once. > I've been looking around, but have so far failed to find a program > which does this. If anyone knows of a program or server which could > handle this, I would be very grateful. > > Cheers, > Ronnie Berntsson >