On Oct 31, 2007, at 2:25 PM, Diep Quang Vinh wrote:

Dear Eric,

Could you please do me an other favor? Could you please tell me how to do your instructions automatic by command line? Since I will deal with a hundreds of files like those and I have to add Hydrogen atom to these file.

Hi Vinh, There is no command-line equivalent for Build Structure, so you have to resort to Python here. Here's the Python code to change the currently selected atom the same way you did by hand: from BuildStructure import changeAtom from chimera import selection, Element changeAtom(selection.currentAtoms()[0], Element("C"), 3, 3, name="C") If you put the above into a script named addCH.py, then you can use these commands to add the hydrogen: sel :2.A@C open C:\<wherever you put the script>\addCH.py You might want to use the "alias" command for the above so you don't have to type so much. --Eric

----- Original Message ----- From: "Eric Pettersen" <pett@cgl.ucsf.edu> To: "Diep Quang Vinh" <vdiep@purdue.edu> Sent: Wednesday, October 31, 2007 4:01 PM Subject: Re: Chimera AddH questions

...

You're welcome. Glad I could help.

--Eric

On Oct 31, 2007, at 12:15 PM, Diep Quang Vinh wrote:

...

Dear Eric,

Thank you very much for your help. It works right now. I appriciate that so much.

Thanks.

Vinh ----- Original Message ----- From: "Eric Pettersen" <pett@cgl.ucsf.edu> To: <vdiep@purdue.edu> Cc: "chimera BB" <chimera-users@cgl.ucsf.edu> Sent: Wednesday, October 31, 2007 2:32 PM Subject: Chimera AddH questions

...

On Oct 31, 2007, at 8:41 AM, chimera-bugs@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@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

Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu