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Derek Smith wrote:
> Dear Tony and Antonello,
> I too had the problem of not getting heteroatoms in my models when I had
> specified HETATM_IO = on. I sorted it out as follows...
> 1. Is the HETATM already parameterised in MODELER?
> if so...

I had the same problem but with modified amino acid residues forming
a chromophore.  Here's my solution.

For simple model building, say the first round with a hetero residue
or just an undefined residue, set these residue types to BLK in the pdb
file and then indicate the positions by . in the alignment both in the
known and unknown sequences. Even if these residues start with ATOM
headers,  Modeller is able to copy the coordinates over and rename
them HETATM.  

For each non-standard residue use a . and for a small molecule use /. 
to indicate that there is no covalent link between the protein and the
BLK residue.

Rename the BLK residues back to their original names and if you had ATOM
headers instead of HETATM, change these back as well in the output.

Good luck!

Shoba Ranganathan, Ph D                             Tel:+61-2-9351-1870
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