[Chimera-users] Disulfide Bond Question

Elaine Meng meng at cgl.ucsf.edu
Wed Feb 16 13:23:29 PST 2011

Hi Wesley,
The current behavior is that you can do this if you are *not* showing the ribbon.  For example, hide the ribbon and then use command "chain @ca".   You could additionally display any other atoms you want, for example with commands such as "disp @n,c,o" or "disp aromatic".

However, if ribbon is displayed, you would need to display the whole cysteine sidechains (except hydrogens, if present), --OR-- manually create connections between the alpha-carbons you already know are involved in the disulfide bond.  You could do the latter by measuring distances between those pairs of alpha-carbons, then Ctrl-click on the distance monitor pseudobond to select it, then clicking the green magnifying glass near the bottom right of the Chimera window to open the Selection Inspector, in which you can change the display properties of the distance monitor pseudobond.

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 Feb 15, 2011, at 5:01 PM, Wesley Chen wrote:

> Hi,
> I can make the disulfide bonds show up between two cysteine resides, but I would like to draw the bond between the two alpha carbons. Right now, I can only draw the disulfide bond itself (which just shows a bar that's parallel to both cysteines) or the whole ball/stick model where all the atoms in the residues show up. I'm just trying to draw a simple bond structure between two cysteines (which is already provided in the pdb file).
> Thanks,
> Wesley

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