Subject: Re: [modeller_usage] Hydrogen name in modeller
From: Modeller Caretaker <>
Date: Mon, 16 Feb 2009 11:18:00 -0800
> It seems that the hydrogen names in Modeller results are HB1, HB2
> However IUPAC and many other software would use 'HB2 HB3' names.
> Is there any options in Modeller that I can choose or any scripts to use to
> convert the format?
Modeller generates output PDB files that are consistent with
post-remediation PDB structures. If you still have software that expects
pre-remediation PDB format, the easiest solution is probably to write a
short script to convert the atom names in the output PDB files.
Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage