[Chimera-users] how to show backbone carbonyl oxygen

Elaine Meng meng at cgl.ucsf.edu
Sat Mar 3 11:48:40 PST 2012

Hard to say without knowing your specific data and exactly what you did to reach that state. Normally you would see the bonds of whatever atomic data you have displayed, in whatever representation you are using.  

But maybe there is something weird about your file and the atoms aren't bonded.  You could doublecheck whether the bonds exist by displaying all atoms, for example by using Presets... interactive 2 (all atoms).  You may want to save the session first, if you have already spent time displaying and coloring things how you want.  If bonds are missing, they can be added with Build Structure (under Tools... Structure Editing) or the command "bond."


On Mar 3, 2012, at 11:29 AM, james09 pruza wrote:

> Dear Dr. Elaine,
> Thanks for the information. I will check that out. One more thing, How to show the ball and stick representation. By default, there are three spheres. I am selecting all  of them and Actions - Atoms and Bonds -  Ball and stick. Nothing happens. Any clue.
> Thanks.
> James
> On Sat, Mar 3, 2012 at 12:35 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi James,
> By default, showing ribbon automatically hides backbone atoms (peptide N,CA,C,O), but you can enable showing them at the same time with the command "ribbackbone."
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html>
> Example commands:
> ribbackbone
> display #0:38 at O
> You can draw a line between any two atoms, but only a straight line.  Actually when you open a file from the PDB of a protein with a missing segment, it will automatically draw a dashed line (for example, PDB 1www), but maybe there is something about your input file that prevents that from happening.  If there is not already a line, a couple of ways to add one are:
> (a) measure distance between the two atoms, then in Distances tool (under Tools... Structure Analysis) set label to "None"... there are several ways to measure the distance, as described here:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances>
> (b) use PseudoBond Reader (under Tools... Depiction) to read in a text file describing the atom pair(s) you want to draw lines between.  Format is described in that page:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html>
> Then to further control display settings of the line, Ctrl-click to select it, then click the magnifying glass in the lower right corner of the Chimera window to show the Selection Inspector, and then inspect "pseudobond" and "pseudobond group" to change various settings.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html>
> 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 Mar 2, 2012, at 9:10 PM, james09 pruza wrote:
> > Hi All,
> > I am using latest Chimera v1.6. I want to show the backbone carbonyl oxygen of one of the residue. The backbone is in ribbon representation.
> > Also, how to make dotted line representation of the missing residues  joining two domains of the same chain.
> > Thanks.
> > James
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