[Chimera-users] how to show backbone carbonyl oxygen

james09 pruza james09xtal at gmail.com
Sat Mar 3 11:29:46 PST 2012

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.


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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