Re: [IMP-users] pdb parser issue in IMP.atom.read_pdb
To: Help and discussion for users of IMP <>
Subject: Re: [IMP-users] pdb parser issue in IMP.atom.read_pdb
From: Daniel Russel <>
Date: Tue, 20 Jul 2010 09:25:53 -0600
Reply-to: Help and discussion for users of IMP <>
I'll relax the check to allow ' characters in atom names.
On Jul 20, 2010, at 6:58 AM, Benjamin SCHWARZ wrote:
You probably know it, but some atom names would simply result in read_pdb to fail. This behavior seems a bit drastic too me. Maybe it would be possible to build a hierarchy containing atoms that could be recognized, and provide some warnings, or give access to the number of encountered errors or ignored atoms when building the hierarchy; leaving the final choice to the user to play with its structure or to reject it.
As an example : pdb code 1E1Q
mh = IMP.atom.read_pdb(pdbFilePath,m)
_IMP.ValueException: Illegal character in atom name, only A-Z, 0-9, " "allowed. Got "HET: O5'"
_______________________________________________ IMP-users mailing list "> https://salilab.org/mailman/listinfo/imp-users