[Chimera-users] how to show backbone carbonyl oxygen

[Elaine Meng]

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