[Chimera-users] Show symmetry axis?

[Oliver Clarke]

Actually never mind… just realized I have requested similar previously and there is already a ticket open (http://plato.cgl.ucsf.edu/trac/chimera/ticket/13829 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/13829>). 

Nevertheless, consider this another vote for constraining fitmap to the symmetry of the input maps (or models) - would be very very helpful when dealing with ion channels.

Cheers,
Oliver.
> 
> Message: 1
> Date: Tue, 13 Oct 2015 20:13:37 -0400
> From: Oliver Clarke <olibclarke at gmail.com>
> To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Subject: [Chimera-users] Show symmetry axis?
> Message-ID: <5DBFD175-0F48-4731-9E7E-C3F635BC571D at gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi all,
> 
> Is there any way to easily generate an axis (of the type created by define axis, not a BILD file) corresponding to the z-axis of a map? Or of the symmetry axis of a map as identified by measure symmetry (which should be the same thing I guess)?
> 
> I would like to be able to align Cn symmetric maps,  which in general have the Cn symmetry axis coincident with z, while strictly obeying the Cn symmetry of the map. 
> 
> There is no built-in way to do this in chimera that I know of, but if I could create an axis corresponding to z for both maps, I could measure correlation between the two maps about that axis, after first aligning the symmetry axes of the two maps and approximately matching their translations along that axis (incidentally, for the same purpose it would be handy to have an additional option for "measure correlation rotationaxis", to measure correlation in a distance range corresponding to +/- x ? from the current position along the specified axis - angleRange is currently present, ?distanceRange? seems like it could be a useful extension).
> 
> The closest I have come so far is the following alias:
> 
> alias ^screen_axis cofr view; savepos tmp; ac mc; namesel z1; clip hither -50;clip yon -50;cofr view; ac mc; namesel z2; sel z1 | z2; define axis sel; ~disp sel; reset tmp
> 
> This will generate an axis perpendicular to and in the center of the screen, but this seems like a bit of a hack? also when I use measure correlation with this axis ("measure correlation #2 #0 rotationAxis a1?, where #2 and #0 are the two maps and the axis is a1),  I get the attached error - is this a bug or did I make a stupid mistake somewhere?
> 
> Cheers,
> Oliver.
> 
> 
> 
> 
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