Missed the first question ;-) ... There is no need to pre-align the sequences for ALIGN2D. Best, Roberto -- Roberto Sanchez, Assistant Professor Structural Biology Program, Department of Physiology & Biophysics and Institute for Computational Biomedicine, Mount Sinai School of Medicine Box 1677, 1425 Madison Avenue, New York, NY 10029 phone +1 (212) 659 8648, fax +1 (212) 849 2456 http://physbio.mssm.edu/~sanchez/ R Senthil Kumar wrote: > Dear friends, > > I am Ph.D student doing my work in the field of protein modelling in > Center for DNA Fingerprinting & Diagnostics(CDFD),Hyderabad,India. > > I am having some doubts about Comparative modelling using modeller > package.Kindly i request you to clear my doubts. > > 1.First thing is before submitting to align2D for alignment the sequences > in the ali file whether it has to be aligned by some sequence alignment > program like clustalW or we can submit the the raw sequence in PIR format > in the ali file to align2D.top file?. > > 2. I am taking three templates for homology modelling for my model.And > one of my template has hetroatoms like glucose(ligands) and i want to > include those hetroatoms to my model.For that i changed my model.top like > this: > > # Homology modelling by the MODELLER TOP routine 'model'. > > INCLUDE # Include the predefined TOP routines > > SET ALNFILE = 'align2d.ali' # alignment filename > SET KNOWNS = '1hkca1' '1hkca2' '1bdg' # codes of the templates > SET SEQUENCE = 'ppgk' # code of the target > SET ATOM_FILES_DIRECTORY = './' # directories for input atom files > SET STARTING_MODEL= 1 # index of the first model > SET ENDING_MODEL = 20 # index of the last model > SET HETATM_IO = ON > > CALL ROUTINE = 'model' # do homology modelling > > But it is not including the hetroatoms in the model.I don't know > why?.Plese help me in this regard. > > from, > Senthil kumar.R > > > > >