[Chimera-users] Show symmetry axis?
Tom Goddard
goddard at sonic.net
Tue Oct 13 18:30:23 PDT 2015
Hi Oliver,
Sounds like your goal is to align to maps with Cn symmetry such that the symmetry axes exactly match. The closest to that is to align the maps and use the Fit Map dialog or fitmap command. But that doesn’t guarantee the symmetry axes exactly match. Since you want to exactly match the axes it seems you need two things, first to define the axis. That sounds like "measure symmetry” because you need a point on the axis that measure symmetry figures out. But that command doesn’t have any option to create an axis. It wouldn’t be too hard to add such an option. Then to optimize the fit you want to allow only translations along the axis and rotations around the axis. Chimera can’t do that. The underlying fitmap code could do it but it would require modifications to the algorithmic code, and command options. All the above things would be nice, but it is too much work to do on Chimera 1 when we are working on Chimera 2.
The error with your “measure correlation” command is that the rotationAxis option does not recognize axes defined by “define axis”. Should give a nice error message explaining that — the traceback instead of a readable error message is a bug.
Tom
> On Oct 13, 2015, at 5:13 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
>
> 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 Å 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.
>
> <PastedGraphic-1.png>
>
>
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