[Chimera-users] Visualizing major and minor axes of inertia

[Felipe Vasquez]

Hi,

I tried to do it using the following bild file (using the info from axes):

.translate 0.0 0.0 0.0
.scale 5
.sphere 0 0 0 0.5
.color 1 0 0
.arrow 0 0 0 0.985 -0.173  -0.013
.color 1 1 0
.arrow 0 0 0 -0.086 -0.553  0.829
.color 0 0 1
.arrow 0 0 0 0.150  0.815  0.559

Because for each axis (v1/v2/v3) there is just one position reported (I
thought they
corresponded to
x2/y2/z2), I
firstly
supposed the x1/y1/z1 in each line of arrow (bild file) should be zero (0).
However, I see now this
assumption
is not correct.
How can I see the arrows superposed on my ligand
?

Regards,

Andres F.


El mié., 5 sept. 2018 a las 1:14, Elaine Meng (<meng at cgl.ucsf.edu>)
escribió:

> Hi Andrés,
> from <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia
> >
>
> "The vectors v1, v2, and v3 are the principal axes (longest to shortest).
> The lengths a, b, c are half-diameters along axes v1, v2, and v3,
> respectively.”
>
> Major is just the longest one.  There isn’t a direct option to show as
> arrows, sorry, only as the ellipsoid.  You could make the ellipsoid
> transparent if that helps (e.g. select it and use command “transparency 75
> sel”).
>
> If it is mainly the directions of the vectors you care about rather than
> the magnitudes, you can (with the atoms selected) instead use commands to
> define a disc that is the plane (first two principal axes) and then the
> normal to that plane (third axis):
>
> define plane sel number 1
> define axis p1
>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
> However, the plane disc size and axis length do not show the vector
> magnitude, only direction.
>
> Another option, but more work, is that you can take the reported values
> from “measure inertia" and calculate arrow endpoints and make a BILD text
> file describing those arrows and open it in Chimera.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html>
>
> You can open the example file linked to that page XYZ-axes.bild (just use
> File… Open) to show the X,Y,Z axes as arrows.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Sep 3, 2018, at 3:26 AM, Felipe Vasquez <anfelvas at gmail.com> wrote:
> >
> > Dear all,
> > I am interested in visualizing the major and minor axes of inertia of a
> ligand in a PDB structure by using UCSF Chimera. Once I calculate the axis
> of inertia by entering in command line:
> >
> > measure inertia sel
> >
> > I obtained the following info (in reply log):
> >
> > v1 =  0.985 -0.173 -0.013   a =  6.079   r1 =  2.103
> >       v2 = -0.086 -0.553  0.829   b =  4.564   r2 =  2.765
> >       v3 = -0.150 -0.815 -0.559   c =  1.127   r3 =  3.400
> >       center =   38.682   56.595   62.547
> >
> > However, I do not still know:
> >
> > 1- What are the major and minor axes of inertia? This info is given by
> the "a/b/c" or "r1/r2/r3" values?
> > 2-How can I visualize the major and minor axes of inertia as planes (or
> arrows)?
> >
> > Thanks in advances for your help.
> > Best regards,
> > Andrés Felipe Vásquez J., BSc, MSc.
>
>
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