[Chimera-users] adding O2 molecule

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 19 11:33:47 PDT 2017

Hi Shumaila,
The email address you should use for Chimera questions is chimera-users at cgl.ucsf.edu (not chimera-bugs etc.).

Please see the previous answer to the same question:

“add bond” will not move the molecule, you have to move it to the right place first (see links in previous answer about how to move it “by hand” with the mouse), before combining into the same model.  Or, instead of combining and using add bond, if it is still a separate model you could try the Join Models  section of Build Structure, which would both move the O2 molecule and automatically add the bond and combine it into the same model.  However, I’m not sure Join Models will work for a bond to a metal ion.  If it doesn’t you would have to use the moving-by-hand approach.

In the previous answer I also suggested a different method, finding a related structure that already has O2 in it, superimposing them, and then copying the O2 coordinates and pasting them into your structure.
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 18, 2017, at 11:06 PM, shumaila <shumailakhan432 at yahoo.com> wrote:
> Hi,
> I want to add oxygen molecule to iron atom in chimera . Kindly help me out how should I add O2 molecule? I tried by Addd bond option but the oxygen molecule is not attached at the desired place. Attached is the protein complex to which I want to attach O2 molecule.Kindly find the attachment.
>                                                            Thank You
> File attachment: pro time_15000ps.pdb
> <pro time_15000ps.pdb>

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