[Chimera-users] Show symmetry axis?

Oliver Clarke olibclarke at gmail.com
Tue Oct 13 19:02:00 PDT 2015

Got it, thanks Tom, yep that's exactly what I want to do... I use fitmap at
the moment, and it is close, but I can tell the match is not symmetric
because the difference map is asymmetric. My apologies for bothering you, I
realized after posting I had asked a similar question previously. Looking
forward to seeing Chimera 2 when it's ready!


On Tue, Oct 13, 2015 at 9:30 PM, Tom Goddard <goddard at sonic.net> wrote:

> 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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