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Thanks, Daniel!
Ben: is it possible to save all warnings/errors in a .err file, so that users can decide if they are something to worry about or not? Natalia Khuri
PhD Student, Graduate Group in Biophysics Laboratory of Andrej Sali UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA From: Daniel Russel [drussel@gmail.com] on behalf of Daniel Russel [drussel@salilab.org]
Sent: Friday, June 29, 2012 8:44 PM To: Khuri, Natalia Cc: List for IMP development Subject: Re: read_pdb in imp 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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