[Chimera-users] Proportional representation of missing segments?

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 28 12:40:52 PDT 2015

Hi Oliver,
Thanks for the suggestion.  Currently there is something like this in a different context: given a query sequence, the MultiDomain Assembler (command “mda”) finds known related structures and arranges them left->right according to N->C of the query.  Where the sequence is not covered by structural data, it draws spheres of different sizes representing the lengths of the gaps.  More info including example images (and another image is attached below):


Not sure if the associated code may be useful, because in that case one is not constrained to connect specific points in space.  Nevertheless, just thought I’d mention it…
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 26, 2015, at 12:36 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> Hi all,
> I think it would be handy, in a future version of chimera, to have an option to represent missing segments in a manner that is proportional to the volume of protein missing - this would be very useful for getting a sense of which chain breaks correspond to very large missing regions (e.g. whole domains), and which correspond to short linkers or loops that are missing.
> For example, in the structure of the ryanodine receptor, there are missing segments ranging in length from ~5-250 residues in length - it would be very handy to be able to get a quick sense, upon first opening a structure, about what fraction of the crystallized or reconstructed protein is actually present in the model.
> I can think of a couple of ways of doing this. One way would be to associate an attribute with each missing segment, corresponding to the number of missing residues, and allow the user to scale the radius, color or opacity of the missing segments in proportion to this value (maybe this attribute already exists somewhere internally?).
> Another way might be to create a completely different missing segment representation - perhaps an ellipsoid, with the ends of the ellipsoid at the N and C-terminal breakpoints, and the volume of the ellipsoid scaled to the volume of a random polymer of the known number of missing residues.
> I would try to do this myself by creating an extension, but I don’t really know where to start to get the information that would be required - I don’t know how to iterate over all missing segments, calculate the number of residues in each, and create a new representation. I guess there is probably a list somewhere in Chimera corresponding to the missing segments and their properties, but I have no idea how to find it.
> Cheers,
> Oliver.

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