Hi Hemant, your problem might be solved by replacing all residues in the alignment that are not present in the pdb file with '-', i.e. with the character indicating a gap. Hope this helps, Oliver hemant kushwaha wrote: > Dear sir, > > I am trying to model a allosteric protein, my problem > is that the number of residues in alignment file(with > template and target sequence) and pdb file is > different b'cos in PDB file there is a gap in the > atoms and HETATM. > > So modeller is giving error at check alignment, and > giving no. of residues in alignment and pdb file are > different. > > Can you please give me any suggestion or advice how to > sort this problem > > with regards > Hemant > > __________________________________ > Do you Yahoo!? > Yahoo! Finance Tax Center - File online. File on time. > http://taxes.yahoo.com/filing.html > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage -- _______________________________________________________________ Oliver Hucke, Dr. Health Sciences Building - K418C University of Washington 1959 NE Pacific St. Dept. of Biochemistry phone: (206) 685 7046 Box 357742 fax : (206) 685 7002 Seattle, WA 98195-7742 email: ohucke@u.washington.edu _______________________________________________________________