[Chimera-users] morph map tool EM density

Franken, L.E. l.e.franken at rug.nl
Thu Apr 14 06:12:06 PDT 2016

Hi Tom,
Thank you for you clear explanation, I managed by fitting 2 structures and
the movie now shows what I intended, but because of the high resolution
structures it feels rather over-interpreted (my maps are around 20A), would
there be a way to filter the morph back to 15A density maps and show that?

Best wishes,

On Wed, Apr 13, 2016 at 8:16 PM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Linda,
>   The Chimera morph map tool just linearly interpolates the density value
> at each map grid point.  So it won’t show a domain rotating if the domain
> moves a long distance — instead it will just disappear in the starting
> position and appear at the final position.  If the motion is small this
> ends up looking like a rotation.  Your start and end maps must have the
> same grid alignment for this to work, in other words if you had to move one
> to align it with the other, then you need to resample the map so it is on
> the same grid points (vop resample command).
>   For your case to show rotation of one monomer relative to the other
> you’d be better off fitting to monomer atomic models into the two maps and
> then use savepos (save position) and reset (restore position) commands to
> smoothly interpolate the atomic model positions between the two
> configurations.  If you fit the two monomers as chains of a single atomic
> model then you would instead use the Morph Conformations tool to
> interpolate.  If you really wanted to see the motion using the maps, you
> could perhaps segment your initial map into two monomer maps, fit the
> segments to the final map, then use savepos/reset to show the motion of the
> two pieces.  There is not tool in Chimera that intelligently moves the
> density from one state to another.  The “Morph” Map name is misleading
> since it does an interpolation, not a morph.
>         Tom
> > On Apr 13, 2016, at 7:16 AM, Franken, L.E. wrote:
> >
> > Hi all,
> > I am fairly new to using chimera and was wondering if there is a way to
> get more control over the path that is calculated when morph map is used
> for two EM density maps that are different conformations. When I use the
> tool now it will change the visible density a great deal and rather than
> rotating only a certain part of the map the result seems quite confusing to
> look at as the whole structures move. Is there a way to fix some areas
> while alowing to morph subregeons? Or does anyone have a better idea on how
> to approach this? the map is a dimer and the change is suposed to be a
> difference in rotation between the two monomers. Ideally I would show this
> by fixing two monomers ontop of each other and allowing the other halfs to
> move.
> >
> > Thank you in advance,
> > Linda
> >
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