Visualizing major and minor axes of inertia
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.* PhD candidate in Chemical Engineering Universidad de los Andes Bogotá, D.C., Colombia Carrera 1 #18A-12, Of. ML-754(26) +57 1 3394949 Ext. 1747
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@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.
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@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@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.
Hi Felipe, You have to do more math than that, sorry. The “center” given in the Log is the center of the ellipsoid, so that is one end of each arrow (x1 y1 z1).
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
The other end is the calculation. The vector (v1, v2, v3) is only the direction (slope) of unit vector (length 1) and a,b,c are the lengths. So you have to back-calculate the other endpoint from the length and the direction... it is not given directly in the Log. For the first principal axis a = 6.079 x1 = 38.682 x2 = 38.862 + 6.079(.985) y1 = 56.595 y2 = 56,595 + 6.079(-.173) z1 = 62.547 z2 = 62.547 + 6.079(-.013) 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 5, 2018, at 3:02 AM, Felipe Vasquez <anfelvas@gmail.com> wrote:
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@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@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.
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
-
Elaine Meng -
Felipe Vasquez