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Hello,

Gly is a good approximation since it has no side chain, but you are positive that you are dealing with some kind of an amino acid residue.

If your PDB file contains the proper 3 letter codes as listed in $MODINSTALL6v2/modlib/restyp.lib, they should be properly recognized in the one letter format too, otherwise Gly...

If you want to have . in your ali, you need to replace ATOM records to HETATM records in your coordinate file for atypical residues. "HETATM_IO =on" effects only HETATM records.

best regards Andras

> Hello, > > Gly is a good approximation since it has no side chain, but you are > positive that you are dealing with some kind of an amino acid residue. > > If your PDB file contains the proper 3 letters codes as listed in > $MODINSTALL6v2/modlib/restyp.lib, they should be properly recognized in > the on eletter format too, otherwise Gly... > > If you want to have . in your ali, you need to replace ATOM records to > recods in your coordinate file for atypical residues. > "HETATM_IO =on" effects only HETATM records. > > best regards > Andras > > Kong Lesheng wrote: > > > > Hi, > > When I use align2d to generate alignment, non-standard residues are always replaced by "G" even I have set "HETATM_IO=ON". > > So in the following modeling, the program will complain that sequence differences between structure and alignment. > > Everytime before I do modeling, I have to manually edit the alignment sequences. > > Could MODELLER automatically write non-standard residues as "." or other symbols which do not affect modeling? > > Thank you very much! > > With best regards, > > Lesheng > > -- > , > Andras Fiser, PhD # phone: (212) 327 7216 > The Rockefeller University # fax: (212) 327 7540 > Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu > New York, NY 10021-6399, USA # http://salilab.org/~andras