[Chimera-users] Molecular representation & FindHbond

[Elaine Meng]

Hi George,
Your dialog shows you chose to find H-bonds between the selection and atom spec, but  you did not enter any atom spec (command-line-style atom specification).  Since the atom spec is blank, the calculation just uses the whole structure.    I'm guessing you meant one of the other choices instead, only find H-bonds  with at least one end selected, or exactly one end selected, or both ends selected.  See:

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html>

By default the C-term carboxyl is treated as an acceptor only.  However, if you really wanted to protonate it you could manually change the atom type of one of the oxygens, for example with a command something like (would change the type of the atom named OXT):

setattr a idatmType O3 @oxt

Then run AddH, then run FindHBond.  However, normally you would not need to add hydrogens before running FIndHBond.  Information on atom types:

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html>

Or, rather than changing the type and adding hydrogens you could just see what atoms are near the C-term carboxyl to "manually" infer whether it could be protonated and H-bonding.  The pKa of that group is fairly low, so I would guess that it is very rarely protonated.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 30, 2011, at 11:41 AM, George Tzotzos wrote:

> Apologies. I did not attach the snapshot. I do so now
> 
> Many thanks
> 
> George
> 
> 
> <snapshot.tiff>
> 
> 
> 
> On May 30, 2011, at 8:25 PM, George Tzotzos wrote:
> 
>> Hi everybody,
>> 
>> I've successfully loaded my protein. It is represented in ribbon.
>> 
>> I want to select three specific residues (e.g. HIS22, TYR53 and VAL124), show them in ball & stick and find Hbonds between them.
>> 
>> I follow the procedure below:
>> 
>> 1. select #0:22,53,124. Chimera returns: 55 atoms, 54 bonds
>> 
>> 2. show sel
>> 
>> 3. repr bs sel
>> 
>> 4. FindHbond (see snapshot). Nothing is displayed. Instead, I see under the command window: 109 hydrogen bonds found. These are ALL the Hbonds found in the protein.
>> 
>> I'd appreciate your guidance how to deal with this.
>> 
>> Another related issue is the carboxy terminal residue. In this case VAL124. It is deprotonated. Is it possible to protonate it and then look for Hbons?
>> 
>> Thanks in advance for your advice
>> 
>> Regards
>> 
>> George
>> 
>> 
>> 
>> 
>> 
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users