[Chimera-users] Chimera AddH questions

Eric Pettersen pett at cgl.ucsf.edu
Wed Oct 31 11:32:56 PDT 2007

On Oct 31, 2007, at 8:41 AM, chimera-bugs at cgl.ucsf.edu wrote:

> The following bug report has been submitted:
> Submitter Name:  Vinh
> Submitter Email: vdiep
> Platform:        windows
> Chimera Version: 1
> Description
> Hello, I would like to ask you some questions concern about addh  
> command.
> 1. I had an molecule which has 2-residues and one of them has an  
> termini -CO. This molecule is in fact was cut from a bigger  
> molecule and the original C have an bond with one H atom. Now Can I  
> by using addh command, recover the original configuration? I mean  
> there is only one Hydrogen added to this Carbon. Since when I did  
> it, chimera gave the an extra Oxigen and not an Hydrogen.

When Chimera looks at a peptide chain with an incomplete C terminus,  
it tries to deduce (by looking at SEQRES records) whether that  
residue is really the C terminus or is instead simply the last  
residue in a chain that is partially missing.  I'm guessing that your  
structure file didn't have any SEQRES records, so Chimera guessed  
that the ending amino acid was really the C terminus and therefore  
made the C-O moiety into a carboxylate.

If all you want to do is add a single hydrogen to that carbon, you  
should use the Build Structure tool to do that.  Here's how:

	control-double click on the carbon
	choose "Modify Atom" from the menu that pops up
	In the Build Structure dialog that comes up, change the "Geometry"  
to "planar" and the "Name" back to "C"
	click on the "Change" button -- your hydrogen will be added

> I try to add the hydrogen for example:
> first : addh
> then : addh spec :2.A at C
> but both of them give me the same answer and on top of that it adds  
> one more H on the other nearby Nitrogen.

The smallest thing addh can add hydrogens to is an entire model.  If  
you specify something smaller, the entire model still gets  
protonated.  This limitation is mentioned in the addh documentation.


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

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