[Chimera-users] creating O2 molecule in Chimera

Elaine Meng meng at cgl.ucsf.edu
Thu Oct 20 11:49:41 PDT 2016

> Subject:	Query about chimera
> Date: 	Thu, 20 Oct 2016 06:47:23 +0000 (UTC)
> From: 	Shumaila Khan <shumailakhan432 at yahoo.com>
> Hello,
>      I m student from Quaid-i-Azam University, Pakistan, doing my MS research project and I have some problems while working on chimera. I want some help regarding Attachment of oxygen atom to plant hemoglobin.Kindly please help me out how will I do that. kindly tell me how to draw oxygen molecule on chimera? While drawing Oxygen molecule it has only only Oxygen atom and two hydrogen atoms attached. Kindly help me out. Waiting for your kind response.

Hi Shumalia, 
Your question was forwarded to me — Chimera questions should be sent to this address, chimera-users at cgl.ucsf.edu 

There are several different approaches you could use.  One way is to use command:

open smiles:oo

If you hold the mouse over it you can see a balloon that says the bond length is 1.004.  You could change the bond length to a better value by
(1) selecting the bond (Ctrl-click on the bond so it has a green outline)
(2) using Build Structure to change the length of the bond.  Menu: Tools… Structure Editing… Build Structure, and in that dialog change from the “Start Structure” section to the “Adjust Bonds” section.  Now you can use the slider or type in a value to change the length to what you want.

That would make the oxygen molecule a separate model from your hemoglobin.  You would probably want to first move the oxygen molecule by hand to the right position, and then (optionally) combine it together with the hemoglobin to make a single model depending on what you are planning to do.  If you don’t need them in the same model, there is no need to combine.

Or, another totally different approach is to find some other hemoglobin structure that already has an oxygen molecule and superimpose the two structures to get the oxygen in the right place, and then delete all the other atoms of the other structure except for the oxygen molecule.

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

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