[Chimera-users] Proportional representation of missing segments?

Oliver Clarke olibclarke at gmail.com
Mon Sep 28 14:24:06 PDT 2015

Thanks Eric and Elaine as always! I will take a look at the documentation
you linked to Eric, this looks interesting and if I have a way to iterate
through all the long bonds I can probably figure something out - I will
post back to the bb if I get something working that I think might be useful
to anyone else out there.


On Mon, Sep 28, 2015 at 5:09 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Oliver,
> This is good idea, but like the mantra you’ve been hearing recently — more
> likely to show up in Chimera 2.  Aside from Elaine’s suggestions, there are
> couple of things you can do in Chimera 1.  By far the easiest is to show
> the sequence for the chain.  The red boxes on the sequence will be as long
> as the number of missing residues.  You could select the residues that
> bookend the box to get an idea of which missing segment it is in the 3D
> model.
> The harder thing, but which you seem willing to try, is to write an
> extension to create an alternate depiction.  Your extension could register
> for the PseudoBond trigger (
> http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_AtomTrigger.html)
> and in your callback function look through the PseudoBond ‘created’ list
> and if pb.category is chimera.LONGBOND_PBG_NAME then that pseudobond is a
> missing segment pseudobond and you can go to town.  One simple thing you
> could do is label the pseudobond with the number of missing residues, e.g.:
> pb.label = str(abs(pb.atoms[0].residue.if.position -
> pb.atoms[1].residue.id.position) - 1) + “ residues”
> While the above is accurate in most situations, there are some where it
> would be slightly off, if say there were insertion codes in the missing
> segment.  A more accurate method would be to look in the chain’s Sequence
> and see how far apart the residues are in the Sequence’s “residues” list.
> Seems a little like overkill, but I’m just putting it out there.
> —Eric
> Eric Pettersen
> UCSF Computer Graphics Lab
> 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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