Missed the first question ;-) ...
There is no need to pre-align the sequences for ALIGN2D.
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
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
> # 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.
> Senthil kumar.R