[Chimera-users] error message

Eric Pettersen pett at cgl.ucsf.edu
Wed Jan 28 11:24:22 PST 2009

On Jan 28, 2009, at 7:22 AM, Katherine Parra wrote:

> Hello!
> I'm trying to get the hydrogen bonds between some selected residues  
> during a trajectory, using per frame commands from tools. But when I  
> get the possible hydrogen bonds formed between the selected residues  
> I also get the following error message in the Reply Log:
> Skipping possible acceptor with bad geometry: #0:2108 at O
> Wrong number of grandchild atoms for phi/psi acceptor #0:2108 at O
> What could be happening?

Hi Katherine,
	A more verbose version of the error message might be:  atom #0:2108 at O  
has been classified as a phi/psi acceptor as per Mills et al (full  
cite in FindHBond docs) but the number of atoms bonded to #0:2108 at O's  
neighbor atoms ("grandchild atoms") is in conflict with that  
	The most likely cause is that #0:2108 at O's bonds are wrong or that its  
neighbor atoms' bonds are wrong.  There is also some chance that  
Chimera has computed the wrong atom type for #0:2108 at O or its  
neighbors.  If you were working with a single structure instead of a  
trajectory then it might also be possible that :2108 is a standard  
residue with missing atoms (Chimera assigns standard residue atom  
types using templates instead of computing them) but trajectories  
typically don't have missing atoms.
	To investigate, you should have a look at #0:2108 at O's atom type and  
it and its neighbor's bonds.  To see the atom type open the command  
lines (Favorites->Command Line) and type "sel #0:2108 at o" and then use  
Actions->Label->IDTAM type.  To see what the atom type means, look at  
this table: Atom Types in Chimera .  If the atom type seems wrong, you  
can change it using the "setattr" command (e.g. to change it to O3,  
type: "setattr a idatmType O3 #0:2108 at o").  If the atom type seems  
okay, look at the bonds and particularly the neighbor's bonds.  If  
there are extra or missing bonds you can fix that using the bond/~bond  
command (type "help bond" in the command line for info).
	You could send me the trajectory to look at if you feel think the  
problem is wrong atom typing or Chimera getting the bonding  
information wrong, and I would try to fix it.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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