[Chimera-users] Disulfide Bond Question

Wesley Chen w.chen89 at gmail.com
Wed Feb 16 13:26:15 PST 2011

Thank you very much! I ended up using the pseudobond method.


On Wed, Feb 16, 2011 at 1:23 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
> ----------
> 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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