[Chimera-users] Including halogen atoms in findHBond tool?

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 23 11:53:14 PDT 2018

Dear Nawei,
I suggest just using distance since we don’t have angle parameters for those in Chimera.  If your structure has hydrogens (or you have added them with the AddH tool or command “addh”), 

… then you can look for hydrogens that are close tof halogen atoms with Find Clashes/Contacts or command “findclash,” e.g. commands:

sel F | Cl | Br | I
findclash sel test "IDATM type.H" overlap -1 hb 0 log true

The first command selects halogen atoms, and has vertical bars (meaning logical OR) between the halogen element symbols.  The findclash command uses “IDATM type.H” because that means polar hydrogens, instead of H for all hydrogens including those attached to carbon.


…then you can see the distance by mousing over the line or looking in the Reply Log (open from Favorites menu).  That finds some pretty long distances, like 3 A; to limit it to shorter distances use an overlap value closer to zero, e.g. “overlap -0.5”

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 23, 2018, at 3:19 AM, Nawel Mele <nawel.mele at gmail.com> wrote:
> Dear Chimera users,
> I am looking for hydrogen bonds between a receptor and an ensemble of docked ligands with different structures including halogen atoms. I would like to know if there is a way to include halogen atoms in the hydrogen bond (findHBond) facility ?
> Best regards,
> Nawel 

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