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

Oliver Clarke olibclarke at gmail.com
Fri Aug 14 15:21:47 PDT 2015

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.


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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20150814/9e56f613/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2015-08-14 18.14.46.png
Type: image/png
Size: 424589 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20150814/9e56f613/attachment.png>

More information about the Chimera-users mailing list