forwarded by the list owner
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Dear All,
My question is regarding the modelling of modified protein residues (i.e. phosphotyrosine: PTR). I know the restype.lib and Modeler libraries contain defintions for some modified residues (e.g selenomethionine) but will not contain them all. For cases like PTR, is it best to define my own residue type within the Modeler libraries or is there a simpler method?
Also, I have query as to the accepted way of dealing with the format of modified residues in PDB files. In PDB files, modified residues are defined within the ATOM coordinates in the correct sequence position but labelled HETATM. I assume its ok to leave them in this format? Does Modeler read them as actual atoms or do you need to change the labelling? My apologies if the answer to this question is rather obvious, I just want to make sure I'm using the accepted format for modified residues.
Many thanks, Karen