[Chimera-users] Hydrogen labeling scheme

Eric Pettersen pett at cgl.ucsf.edu
Wed Feb 19 13:12:45 PST 2020

Hi Jack,
	Chimera tries to use hydrogen names that follow PDB-standard naming if possible.  That means the hydrogen name is the same as the heavy atom it’s attached to, with the chemical-element part of the heavy atom name replaced with ‘H’ and with digits appended if multiple hydrogens are being added to the atom (or primes [‘] if the heavy atom name ends with a prime).  It handles well-known exceptions to the rule (e.g. hydrogens added to N6 in ATP are HN61 and HN62).  The digits added don’t necessarily start at 1 — if adding two hydrogens to an atom with two other heavy atoms bonded to it, the numbering starts at 2.  This is all for PDB version 3.  There are some additional rules for PDB version 2 which you probably have no need to know since PDB version 2 is ancient at this point.
	For some structures (e.g. some small molecules), the above scheme doesn’t work either because prerequisites are lacking (e.g. atom names don’t start with the atomic symbol) or the resulting hydrogen names aren’t unique.  Depending on the issue, a fallback approach is used:

1) Names don't start with atomic symbol or heavy atom names not unique within the residue:  prepend the heavy atom atomic symbol with ‘H’ and add digits as needed to make the name unique within the residue.

2) Otherwise: for atoms where the post-atomic-symbol part of the name is unique within the residue, replace the atomic symbol with ‘H’, otherwise prepend ‘H’.  In both cases add digits if multiple hydrogens being added to atom.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Feb 14, 2020, at 12:44 PM, Jack Fuller <jtfuller at chem.ucla.edu> wrote:
> Hello,
> I am part of a computational chemistry research group that frequently uses chimera to add hydrogens to pdbs.  My coworkers and I have noticed that chimera uses several different labeling schemes for hydrogens.  We have been unable to determine how chimera chooses which scheme to use.  Is there a way to specify which scheme to use or to know which scheme chimera will choose?
> Thank you,
> Jack Fuller
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