One gets warnings like that when atoms are read from the PDB whose atom type (the 3rd entry on an ATOM line in the PDB file) is something non-standard or incorrect. They aren't necessarily worth worrying about, depending on what you want to do with the file. We could, perhaps, provide the residue type and index in the error message which might make the message easier to deal with (Ben would know more). However, there is a tradeoff as the warnings in PDB reading are collapsed to only print out each warning once and files with an unknown atom type often have many of the same unknown atom type. So adding the residue index might results in lots and lots of warnings :-) On Jun 29, 2012, at 7:53 PM, Khuri, Natalia wrote:
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