Suggestion - secondary structural element as an additional level in the selection hierarchy?
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.
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. Best, 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 Jul 3, 2014, at 3:58 PM, Oliver Clarke <olibclarke@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.
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@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.
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@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@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.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Eric Pettersen -
Oliver Clarke