[Chimera-users] Suggestion - secondary structural element as an additional level in the selection hierarchy?

Elaine Meng meng at cgl.ucsf.edu
Thu Jul 3 16:33:10 PDT 2014

Hi Oliver,
Not the same, but...
the current route to something similar is to show Sequence (under Favorites menu) for the chain of interest, then manually drag a box on the sequence to select the desired helix, strand, or loop segment.  The sequence window shows helices and strands as light yellow and light green boxes, respectively.

You could first select on the structure to see where the selection is in the sequence, then select in the sequence window.
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 3, 2014, at 3:58 PM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Greetings,
> Currently, the selection hierarchy in Chimera is as follows - atom<residue<chain<model<all.
> I don’t know how complicated it would be to implement, but perhaps it might be desirable in a future version of Chimera to include “secondary structural element” (being coil, helix or strand) as an additional level, between residue and chain?
> This would enable easy/quick selection/coloring of specific loops, helices or strands in a structure. 
> E.g, say I am working on a helical repeat protein like an importin, and I want to color all the helices on the concave, inside surface one color, and all the helices on the outside surface another color - to do that at present is possible, but somewhat laborious, as it is necessary to explicitly specify the boundaries of each helix, and if there are many helices in the desired selection that are not sequence-adjacent then this becomes complicated. 
> If SSE was a level of the selection hierarchy, I could select one residue in each helix on the desired surface, press the up arrow once to broaden the selection and all the helices on the inner surface would then be selected, without needing to know the location in the sequence of each helix.
> It seems like there would be quite a lot of use cases where this might save time - selecting individual surface exposed loops, or a specific set of helices or strands that form a binding surface for a ligand or partner protein, for example.
> Best regards,
> Oliver.

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