[Chimera-users] How to change water molecule from triangle stick to folded line stick?

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 12 10:17:17 PDT 2013

Hello, Hyeona!
Water molecules are sometimes defined with the extra H-H bond, to help them hold their shape during simulations.  

However, in Chimera you can just hide those bonds, for example with command:

bonddisplay off :wat&H

(show command line using menu: Favorites... Command Line)

You could also delete them, although you might not want to do that if you might do energy calculations later or save the file for energy calculations in some other program.  If you are sure you won't need the bonds later, you could delete them with command:

~bond :wat&H

Whether or not the bond is shown, you can still use any display style for the molecules: stick, ball&stick, sphere ...

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

On Mar 12, 2013, at 12:25 AM, 강현아 wrote:

> Hello, Chimera Users!
> I am just a beginner and haven’t learned much about Chimera.
> When I load water molecules in Chimera main window, (TIP3P water) they have triangle shape.
> Then, I have changed option to stick or ball&stick. (action>atoms/bonds>stick or ball&stick)
> But, they are still triangle. It looks like there is H-H covalent bond in H2O.
> How can I remove this unwanted bond?
> Is there any other option for molecule shape? Like licorice…
> Please let me know how can I draw water with folded line stick shape, not triangle.
> Thanks in advance.
> Best regards,
> Hyeona Kang

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