[Chimera-users] Force stick representation of a residue in ribbon display

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 15 09:53:59 PDT 2016


Dear Juan,
After “ribbackbone” you can then hide (undisplay) any subset of the atoms.  However, then the problem then is that ribbon does not pass through the exact positions of the atoms, so the remaining C=O and the CA atoms of any displayed sidechains may be floating away from the ribbon.   E.g. try commands:

ribbackbone
~disp @n,c,o
disp :71 at c,o
setattr m autochain 0

You may be able to see the “floating away” problem, described in more detail here: 
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset>

Possible solutions:
(1) if the CAs and C are pretty close to the ribbon, you could make either or both into balls so that it is less obvious they are detached, e.g. command: repr bs @ca,c

- and-/or -
(2) use “ribspline” to make the ribbon go through the CA positions, e.g. command: ribspline cardinal smooth strand
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html>
(if you don’t like the resulting ribbon, you can change it back to the default with command: ribspline b)

- or -
(3) open two copies of the structure, one showing ONLY the ion and the C=O of THR 71 (not ribbon) and the other showing the ion, ribbon and other sidechains (without ribbackbone).  In that case the C=O may still appear to be detached but at least all of the sidechains will be joined to the ribbon.

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 15, 2016, at 8:50 AM, Eiros Zamora, Juan <j.eiros-zamora14 at imperial.ac.uk> wrote:
> 
> Dear Chimera experts, 
> Is it possible to show in stick representation the C=O bond of the backbone of a residue while maintaning the ribbon representation of the backbone? I’ve tried setting on the ‘ribbackbone’ command, but that activates all the backbone atoms for  other stick-displayed atoms, and I want to avoid that. 
> 
> <image1.png><image2.png>
> 
> I’m attaching two images to clarify what I mean. Basically, to keep it as image1 but displaying the C=O bond of THR 71, to make the 2.88 Å distance clearer.
> 
> Any help on this matter will be greatly appreciated.
> Best, 
> Juan




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