The problem is that Chimera "knows" the atom types of standard residues and doesn't try to compute them from scratch. Therefore it assigns ND1 in HIS a sp2 type, which throws a monkey wrench into the find-hbond computation as it looks for the planarity of the ND1 and sees it bonded to nothing!

For what you want to do, you want to get that atom's residue changed. Do this:

1) Control-double click on the ND1 atom

2) Chose "Modify Atom" from the resulting popup menu.

3) Change the "Element" to "N"; leave "Geometry" as "tetrahedral"

4) Change "Bonds" to 3

5) In the "Residue Name" section, use the "new residue" option with "NH3" as the name and chain "het"

5) Click the Change button

That should give you what you want.

Eric Pettersen

UCSF Computer Graphics Lab

http://www.cgl.ucsf.edu

On May 22, 2008, at 10:25 AM, Tyler Arbour wrote:

Wow, I didn't expect a response for this...great! I was actually just trying to create a figure representing a computational model that I am using. Starting from the crystal structure, I wanted to actually change the histidinal N to a simple NH3 molecule. I am just trying to get familiar with Chimera--I usually use DS Viewerpro for modifying structures, and it doesn't seem like Chimera is well-suited to this type of modification. If you have any advice on an easy way to make this conversion so that I have a nice figure, I'd greatly appreciate it! Thanks.

Tyler

On May 22, 2008, at 11:17 AM, Eric Pettersen wrote:

Hi Tyler,
Your structure seems to have a histidine residue (residue 159 in chain A) that consists solely of an ND1 atom! How did you manage that?

--Eric

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