[Chimera-users] Modification of ribbon scaling to intersect guide atoms at termini and chain breaks?

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 14 15:38:47 PDT 2015


Hi Oliver,
I agree it would be nicer to have finer control of the ribbon path, and we are keeping things like this in mind while designing how ribbons should work in Chimera2.

However, in the meanwhile in Chimera1, the closest thing to what you are describing is cardinal spline but with smoothing of strands and/or helices (loops and non-helix non-strand termini remaining unsmoothed).  Besides the smoothing, there is also a stiffness parameter, but in practice even trying combinations of values, I find that the strands don’t look quite as nice as in the B-spline.

<http://www.rbvi.ucsf.edu/chimera/features.html#ribspline>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html>

My typical compromise is command: 
ribspline card smooth strand

Thanks for your thoughts and example,
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 Aug 14, 2015, at 3:21 PM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Suggestion - would it be possible at some point in the future to add a new ribbon scaling option (I guess in Chimera 2.0 or later) so that all internal residues behave like the current “Bspline” scaling, but residues at termini or chain breaks behave like “cardinal” - where the ribbon path exactly intersects the guide atoms? 
> 
> The attached image illustrates the kind of situation this would address - where one wants to show secondary structure in cartoon, but pick out a  loop or structural feature of interest in backbone or CA+sidechains, with no ugly discontinuities between the all-atom and ribbon representations.
> 
> This would allow seamless mixing of nice looking cartoon representation and nice looking backbone or C-alpha+sidechains representation, which I don’t believe is possible at the moment.
> 
> Cheers,
> Oliver.
> 
> Also, in case anyone finds it useful, the following alias applied to a selection or model will generate the CA+sidechains representation depicted below:
> 
> #Show CA trace with sidechains
> #Usage: ca_and_sidechains #model_id (or selection/atom-spec)
> alias ^ca_and_sidechains sel $1; namesel tmp; ~ribbon tmp; ~disp tmp; sel tmp&@CA&protein; repr stick sel; disp sel; setattr m stickScale 1.00
>  tmp;  sel side chain/base.without CA/C1'&tmp; repr stick sel; disp sel; setattr b radius 0.1 sel; color orange tmp; color byhet tmp; sel @CAA
> |@CB; namesel tmp2; sel tmp&tmp2; repr stick sel; setattr b radius 0.1 sel; sel @CD,N&:pro&tmp; disp sel; repr stick sel; setattr b radius 0..
> 1 sel; ~sel
> 
> <Screenshot 2015-08-14 18.14.46.png>
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