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We did something like this with esprit. You get the sequence alignments from Psiblast or whatever you fancy, then edit in the structural alignment into the txt file it generates. Messy but successful.. Eleanor On 12/01/2010 03:44 PM, Gerard DVD Kleywegt wrote: > This was one of the things that Indonesia was written for (a long time > ago, in a galaxy far, far away), although I'm not sure if it will still > run. If you're desperate, see http://xray.bmc.uu.se/~dennis/ > > --Gerard > > > > On Fri, 26 Nov 2010, Muhammed bashir Khan wrote: > >> Dear All; >> >> I have structures of two protein one full-length while the other >> truncated >> at the c-terminus(one from prokaryote while the other from eukaryotes). >> Now I want to do the sequence alignment of these two proteins from all >> species in such a way that the structure based sequence remain constant >> while extending the sequence only at the c-terminus. Remember the >> structure are known only for the two proteins. >> >> Any suggestion will be highly appreciated!!!!! >> >> Regards and have a nice weekend. >> >> Bashir >> > > > Best wishes, > > --Gerard > > ****************************************************************** > Gerard J. Kleywegt > Dept. of Cell & Molecular Biology University of Uppsala > Biomedical Centre Box 596 > SE-751 24 Uppsala SWEDEN > > http://xray.bmc.uu.se/gerard/ mailto:[log in to unmask] > ****************************************************************** > The opinions in this message are fictional. Any similarity > to actual opinions, living or dead, is purely coincidental. > ******************************************************************