[Chimera-users] Ellipsoid using chimera

[Anu Chandran]

Thank you very much....

On Mon, Oct 20, 2014 at 9:34 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> For both methods, it is important to only include the atoms you really
> want to include.  For example, you would not want to specify  an entire
> model or chain if it includes stuff like waters and ligands.  You could
> specify just the part you want as a residue number range, or as
> protein-only.  Consider also whether you want to include sidechain atoms or
> just the backbone.
>
> Elaine
>
> On Oct 20, 2014, at 8:56 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
> > Dear Anu,
> > The "measure inertia" command reports the axes in the Reply Log (menu:
> Favorites… Reply Log).   So it would be possible to manually calculate
> angles from those values.
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia
> >
> >
> > However, in my opinion, it would be easier to use "define axis"  or
> "define plane" on each of the domains (or the corresponding GUI, menu:
> Tools… Structure Analysis… Axes/Planes/Centroids).  That would create
> best-fit axis or plane objects on which you can easily perform measurements
> of distances and angles using either the Axes/Planes/Centroids GUI or the
> "distance" and "angle" commands.
> >
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes
> >
> >
> > Differences:
> > - Axes/Planes/Centroids doesn't make ellipsoids, it just calculates a
> best-fit axis or a best-fit plane… but you could still use the "measure
> inertia" ellipsoids for display
> >
> > - "measure inertia" always uses mass-weighting for atoms, whereas
> Axes/Planes/Centroids doesn't mass-weight by default, but there are command
> and GUI options to turn it on
> >
> > - if you use the same atoms and same parameters (e.g. mass-weighting), I
> believe the directions of the Axes/Planes/Centroids axis and the ellipsoid
> longest axis would be the same, and thus angles calculated from the two
> methods should be in agreement.  The lengths could be different because
> they are determined in different ways.  It is a similar situation for the
> ellipsoid two longest axes and the Axes/Planes/Centroids plane.
> >
> > - Axes/Planes/Centroids  works only on atoms, not input surfaces,
> whereas "measure inertia" could work if you only had some surface without
> atoms… but this doesn't sound relevant to your situation anyway
> >
> > I hope this helps,
> > Elaine
> > ----------
> > Elaine C. Meng, Ph.D.
> > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > On Oct 19, 2014, at 9:31 PM, Anu Chandran <miscofanu at gmail.com> wrote:
> >
> >> Dear users,
> >> I have used chimera to draw ellipsoid to represent each domain in a
> protein structure using the measure inertia command in an attempt to
> visualize the orientation of one domain with respect to the other. This has
> been done for a set of homologous structures of the same protein.
> >>
> >> Now I want to visualize the axes of the ellipsoid of the two domains.
> Can anybody please suggest me on how to do it ?
> >>
> >> Also Is there any way to quantitate the angle between the two ellipsoid
> representing the two domains in a protein ?
> >>
> >> Thanking you,
> >>
> >> with regards,
> >> Anu
> >
> >
> > _______________________________________________
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> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
>
>
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