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

Eric Pettersen pett at cgl.ucsf.edu
Mon Jul 7 17:42:20 PDT 2014


I have added an "sse element" level in the selection hierarchy.  It will be available in tonight's daily build (look for builds dated July 8th or later).  Let me know if you run into any rough edges. ;-)

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jul 4, 2014, at 8:21 AM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Hello,
> 
> An alternative, perhaps simpler way of accomplishing the same behavior might be to add a “thisSSE” selector, which would select any secondary structural elements (helices, strands, or coils) that intersect with the current selection.
> 
> Best,
> Oliver.
> On Jul 3, 2014, at 6:58 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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