Hi Elaine, Thanks for your great response. It is really helpful. Could I ask more questions? Based on your direction, I already figured out how to define the axes and planes and then use 'angle' command to measure the angles between them. However, it may induce a bit of a bias by defining the axes manually. Could the ChimeraX generate a more accurate axis automatically that is through the mass center of the molecule? For instance, the command 'measure inertia #1/A showEllipsoid true' can generate the ellipsoid that is oriented based on the principal axes of inertia. I assume that the principal axis of inertia is through the mass center of the molecule. [cid:02527f1c-d0cc-4820-bb2d-1c02b8cf4ec0] What I need is to generate axes like the black and red lines that go through the center of mass of the molecule and divide it into two equal parts. So how do I get this? Below is the output after I ran the command 'measure inertia' to show the ellipsoid of two subunits of a complex. measure inertia #1/A showEllipsoid true Inertia axes for 8dzs, 2074 atoms v1 = -0.508 -0.554 0.659 a = 36.027 r1 = 12.001 v2 = 0.356 -0.832 -0.425 b = 19.480 r2 = 18.103 v3 = 0.784 0.019 0.620 c = 18.455 r3 = 18.316 center = 125.9 126.14 150.23 measure inertia #1/b showEllipsoid true Inertia axes for 8dzs, 1641 atoms v1 = 0.520 0.842 0.141 a = 39.590 r1 = 11.344 v2 = -0.329 0.045 0.943 b = 18.123 r2 = 19.403 v3 = 0.788 -0.537 0.301 c = 17.747 r3 = 19.472 center = 148.04 146.61 117.1 The output shows three vectors, v1, v2, and v3 and the mass center of the subunit. My question is whether the v1 vector represents the direction of the black line of subunit A. If it is, I can define the axis based on the two coordinates (0,0,0) and ( -0.508,-0.554, 0.659) for unit A, and the coordinates (0,0,0) and ( 0.520,0.842, 0.141) for subunit B. After this, I can use the command 'angle' to calculate the angles between two axes. Is my understanding correct? Please let me know if it is, or share your strategy when you have a chance. Thank you very much. Looking forward your response, Jianming ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Sunday, February 23, 2025 10:44 AM To: junjie han <hanjunjie2014@gmail.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: Measure angle between domains in chimeraX Hi Junjie, In general there are two ways: (1) use Define Axes/Planes/Centroids tool or "define" command to define axis or plane objects based on specified atoms. Then you can get the crossing angles between any pairs of these objects using the Axes/Planes/Centroids GUI or the "angle" command. See the following for details: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/axesplanes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html> (2) if the two domains are structurally similar to each other, you could open two copies of the structure and fit one onto the other, superimposing the parts you want to superimpose (using whatever method you want, "align" or "matchmaker" or manual movements). Then you can get the relationship between the two models with "measure rotation" -- see the following for details: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Feb 22, 2025, at 8:39 PM, junjie han <hanjunjie2014@gmail.com> wrote:

Hi Elaine,

I hope this email finds you well. May I ask how to measure the angle between two domains from one molecule or two different molecules in ChimeraX. Here are some examples below. Example 1:

<image.png>How to calculate these angles (54°, 38°)？

Example 2:<image.png>How to calculate this angle (75°) ?

Example 3:<image.png>How can I measure the rotation angle between A and B, or between two specific regions of these two molecules in ChimeraX? If I need to calculate the rotation angles of two molecules relative to a specific molecule, how can I define a shared axis for calculating the rotation angles? The rotation axes are different when I use the command “measure rotation A toModel B” to calculate the rotation angles, which is not an ideal way to compare them in parallel.

Thank you in advance for your any suggestions.

Very appreciated, Junjie

You could just use "define axis" with "massWeighting true" -- as far as I know, it should give the same principal axis as "measure inertia" for the same set of atoms. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#inertia> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#axis> Both commands take specified atoms, so they are equally "biased," if by biased you mean based on the atoms you specified. You can specify all atoms in the model if that's what you want, but it would really include everything like waters, ligand, etc. The "measure inertia" help explains the output (v1, v2, v3 etc.) and yes the first one is the longest one. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#inertia> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Feb 23, 2025, at 2:46 PM, junjie han <hanjunjie2014@gmail.com> wrote:

Hi Elaine,

Thanks for your great response. It is really helpful. Could I ask more questions? Based on your direction, I already figured out how to define the axes and planes and then use 'angle' command to measure the angles between them. However, it may induce a bit of a bias by defining the axes manually. Could the ChimeraX generate a more accurate axis automatically that is through the mass center of the molecule? For instance, the command 'measure inertia #1/A showEllipsoid true' can generate the ellipsoid that is oriented based on the principal axes of inertia. I assume that the principal axis of inertia is through the mass center of the molecule.<image.png>What I need is to generate axes like the black and red lines that go through the center of mass of the molecule and divide it into two equal parts. So how do I get this?

Below is the output after I ran the command 'measure inertia' to show the ellipsoid of two subunits of a complex.

measure inertia #1/A showEllipsoid true Inertia axes for 8dzs, 2074 atoms v1 = -0.508 -0.554 0.659 a = 36.027 r1 = 12.001 v2 = 0.356 -0.832 -0.425 b = 19.480 r2 = 18.103 v3 = 0.784 0.019 0.620 c = 18.455 r3 = 18.316 center = 125.9 126.14 150.23

measure inertia #1/b showEllipsoid true Inertia axes for 8dzs, 1641 atoms v1 = 0.520 0.842 0.141 a = 39.590 r1 = 11.344 v2 = -0.329 0.045 0.943 b = 18.123 r2 = 19.403 v3 = 0.788 -0.537 0.301 c = 17.747 r3 = 19.472 center = 148.04 146.61 117.1

The output shows three vectors, v1, v2, and v3 and the mass center of the subunit. My question is whether the v1 vector represents the direction of the black line of subunit A. If it is, I can define the axis based on the two coordinates (0,0,0) and ( -0.508,-0.554, 0.659) for unit A, and the coordinates (0,0,0) and ( 0.520,0.842, 0.141) for subunit B. After this, I can use the command 'angle' to calculate the angles between two axes. Is my understanding correct? Please let me know if it is, or share your strategy when you have a chance. Thank you very much.

Looking forward your response, Jianming

From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Sunday, February 23, 2025 10:44 AM To: junjie han <hanjunjie2014@gmail.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: Measure angle between domains in chimeraX Hi Junjie, In general there are two ways:

(1) use Define Axes/Planes/Centroids tool or "define" command to define axis or plane objects based on specified atoms. Then you can get the crossing angles between any pairs of these objects using the Axes/Planes/Centroids GUI or the "angle" command. See the following for details: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/axesplanes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html>

(2) if the two domains are structurally similar to each other, you could open two copies of the structure and fit one onto the other, superimposing the parts you want to superimpose (using whatever method you want, "align" or "matchmaker" or manual movements). Then you can get the relationship between the two models with "measure rotation" -- see the following for details: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Feb 22, 2025, at 8:39 PM, junjie han <hanjunjie2014@gmail.com> wrote:

Hi Elaine,

I hope this email finds you well. May I ask how to measure the angle between two domains from one molecule or two different molecules in ChimeraX. Here are some examples below. Example 1:

<image.png>How to calculate these angles (54°, 38°)？

Example 2:<image.png>How to calculate this angle (75°) ?

Example 3:<image.png>How can I measure the rotation angle between A and B, or between two specific regions of these two molecules in ChimeraX? If I need to calculate the rotation angles of two molecules relative to a specific molecule, how can I define a shared axis for calculating the rotation angles? The rotation axes are different when I use the command “measure rotation A toModel B” to calculate the rotation angles, which is not an ideal way to compare them in parallel.

Thank you in advance for your any suggestions.

Very appreciated, Junjie

Hi Elaine, Thank you. Could you please help to confirm that whether the v1 vector represents the direction of the axis defined based on the two coordinates (0,0,0) and ( -0.508,-0.554, 0.659) for the subunit A? If so, is the defined axis parallel to the direction of the black line that divides subunit A into two equal parts? measure inertia #1/A showEllipsoid true Inertia axes for 8dzs, 2074 atoms v1 = -0.508 -0.554 0.659 a = 36.027 r1 = 12.001 v2 = 0.356 -0.832 -0.425 b = 19.480 r2 = 18.103 v3 = 0.784 0.019 0.620 c = 18.455 r3 = 18.316 center = 125.9 126.14 150.23 [cid:3a6862b1-7306-4c90-b4c4-e322ecd6652e] Please let me know when you have a chance. Very appreciated, Junjie ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, February 24, 2025 10:34 AM To: junjie han <hanjunjie2014@gmail.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: Measure angle between domains in chimeraX You could just use "define axis" with "massWeighting true" -- as far as I know, it should give the same principal axis as "measure inertia" for the same set of atoms. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#inertia> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#axis> Both commands take specified atoms, so they are equally "biased," if by biased you mean based on the atoms you specified. You can specify all atoms in the model if that's what you want, but it would really include everything like waters, ligand, etc. The "measure inertia" help explains the output (v1, v2, v3 etc.) and yes the first one is the longest one. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#inertia> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Feb 23, 2025, at 2:46 PM, junjie han <hanjunjie2014@gmail.com> wrote:

Hi Elaine,

Thanks for your great response. It is really helpful. Could I ask more questions? Based on your direction, I already figured out how to define the axes and planes and then use 'angle' command to measure the angles between them. However, it may induce a bit of a bias by defining the axes manually. Could the ChimeraX generate a more accurate axis automatically that is through the mass center of the molecule? For instance, the command 'measure inertia #1/A showEllipsoid true' can generate the ellipsoid that is oriented based on the principal axes of inertia. I assume that the principal axis of inertia is through the mass center of the molecule.<image.png>What I need is to generate axes like the black and red lines that go through the center of mass of the molecule and divide it into two equal parts. So how do I get this?

Below is the output after I ran the command 'measure inertia' to show the ellipsoid of two subunits of a complex.

measure inertia #1/A showEllipsoid true Inertia axes for 8dzs, 2074 atoms v1 = -0.508 -0.554 0.659 a = 36.027 r1 = 12.001 v2 = 0.356 -0.832 -0.425 b = 19.480 r2 = 18.103 v3 = 0.784 0.019 0.620 c = 18.455 r3 = 18.316 center = 125.9 126.14 150.23

measure inertia #1/b showEllipsoid true Inertia axes for 8dzs, 1641 atoms v1 = 0.520 0.842 0.141 a = 39.590 r1 = 11.344 v2 = -0.329 0.045 0.943 b = 18.123 r2 = 19.403 v3 = 0.788 -0.537 0.301 c = 17.747 r3 = 19.472 center = 148.04 146.61 117.1

The output shows three vectors, v1, v2, and v3 and the mass center of the subunit. My question is whether the v1 vector represents the direction of the black line of subunit A. If it is, I can define the axis based on the two coordinates (0,0,0) and ( -0.508,-0.554, 0.659) for unit A, and the coordinates (0,0,0) and ( 0.520,0.842, 0.141) for subunit B. After this, I can use the command 'angle' to calculate the angles between two axes. Is my understanding correct? Please let me know if it is, or share your strategy when you have a chance. Thank you very much.

Looking forward your response, Jianming

From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Sunday, February 23, 2025 10:44 AM To: junjie han <hanjunjie2014@gmail.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: Measure angle between domains in chimeraX Hi Junjie, In general there are two ways:

(1) use Define Axes/Planes/Centroids tool or "define" command to define axis or plane objects based on specified atoms. Then you can get the crossing angles between any pairs of these objects using the Axes/Planes/Centroids GUI or the "angle" command. See the following for details: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/axesplanes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html>

(2) if the two domains are structurally similar to each other, you could open two copies of the structure and fit one onto the other, superimposing the parts you want to superimpose (using whatever method you want, "align" or "matchmaker" or manual movements). Then you can get the relationship between the two models with "measure rotation" -- see the following for details: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Feb 22, 2025, at 8:39 PM, junjie han <hanjunjie2014@gmail.com> wrote:

Hi Elaine,

I hope this email finds you well. May I ask how to measure the angle between two domains from one molecule or two different molecules in ChimeraX. Here are some examples below. Example 1:

<image.png>How to calculate these angles (54°, 38°)？

Example 2:<image.png>How to calculate this angle (75°) ?

Example 3:<image.png>How can I measure the rotation angle between A and B, or between two specific regions of these two molecules in ChimeraX? If I need to calculate the rotation angles of two molecules relative to a specific molecule, how can I define a shared axis for calculating the rotation angles? The rotation axes are different when I use the command “measure rotation A toModel B” to calculate the rotation angles, which is not an ideal way to compare them in parallel.

Thank you in advance for your any suggestions.

Very appreciated, Junjie

Hi Tom, Thank you for your confirmation. Yes, my need is to measure the angle between the two longest axes, not the total rotation from one structure to the other structure. By the way, do you know how to align the center of subunit A to the coordinate (0,0,0), and then make the subunit A parallel to the z axis? Thank you very much, Junjie ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Monday, February 24, 2025 12:56 PM To: junjie han <hanjunjie2014@gmail.com> Cc: chimerax-users <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Measure angle between domains in chimeraX Hi Junjie, Yes that vector is the long axis of the inertia ellipsoid computed for the chain A atoms. If you measure the angle between that long axis for two structures be aware that it is not the total rotation to move one structure to the other because the structure may also need to rotate about the axis to move one structure to the other. Maybe you want the angle between the long axes. But if instead you want the total rotation to move one structure to another then you should align the the structures and use "measure rotation" as Elaine suggested earlier. Tom On Feb 24, 2025, at 10:25 AM, junjie han via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hi Elaine, Thank you. Could you please help to confirm that whether the v1 vector represents the direction of the axis defined based on the two coordinates (0,0,0) and ( -0.508,-0.554, 0.659) for the subunit A? If so, is the defined axis parallel to the direction of the black line that divides subunit A into two equal parts? measure inertia #1/A showEllipsoid true Inertia axes for 8dzs, 2074 atoms v1 = -0.508 -0.554 0.659 a = 36.027 r1 = 12.001 v2 = 0.356 -0.832 -0.425 b = 19.480 r2 = 18.103 v3 = 0.784 0.019 0.620 c = 18.455 r3 = 18.316 center = 125.9 126.14 150.23 <image.png> Please let me know when you have a chance. Very appreciated, Junjie ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, February 24, 2025 10:34 AM To: junjie han <hanjunjie2014@gmail.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: Measure angle between domains in chimeraX You could just use "define axis" with "massWeighting true" -- as far as I know, it should give the same principal axis as "measure inertia" for the same set of atoms. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#inertia> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#axis> Both commands take specified atoms, so they are equally "biased," if by biased you mean based on the atoms you specified. You can specify all atoms in the model if that's what you want, but it would really include everything like waters, ligand, etc. The "measure inertia" help explains the output (v1, v2, v3 etc.) and yes the first one is the longest one. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#inertia> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Feb 23, 2025, at 2:46 PM, junjie han <hanjunjie2014@gmail.com> wrote:

Hi Elaine,

Thanks for your great response. It is really helpful. Could I ask more questions? Based on your direction, I already figured out how to define the axes and planes and then use 'angle' command to measure the angles between them. However, it may induce a bit of a bias by defining the axes manually. Could the ChimeraX generate a more accurate axis automatically that is through the mass center of the molecule? For instance, the command 'measure inertia #1/A showEllipsoid true' can generate the ellipsoid that is oriented based on the principal axes of inertia. I assume that the principal axis of inertia is through the mass center of the molecule.<image.png>What I need is to generate axes like the black and red lines that go through the center of mass of the molecule and divide it into two equal parts. So how do I get this?

Below is the output after I ran the command 'measure inertia' to show the ellipsoid of two subunits of a complex.

measure inertia #1/A showEllipsoid true Inertia axes for 8dzs, 2074 atoms v1 = -0.508 -0.554 0.659 a = 36.027 r1 = 12.001 v2 = 0.356 -0.832 -0.425 b = 19.480 r2 = 18.103 v3 = 0.784 0.019 0.620 c = 18.455 r3 = 18.316 center = 125.9 126.14 150.23

measure inertia #1/b showEllipsoid true Inertia axes for 8dzs, 1641 atoms v1 = 0.520 0.842 0.141 a = 39.590 r1 = 11.344 v2 = -0.329 0.045 0.943 b = 18.123 r2 = 19.403 v3 = 0.788 -0.537 0.301 c = 17.747 r3 = 19.472 center = 148.04 146.61 117.1

The output shows three vectors, v1, v2, and v3 and the mass center of the subunit. My question is whether the v1 vector represents the direction of the black line of subunit A. If it is, I can define the axis based on the two coordinates (0,0,0) and ( -0.508,-0.554, 0.659) for unit A, and the coordinates (0,0,0) and ( 0.520,0.842, 0.141) for subunit B. After this, I can use the command 'angle' to calculate the angles between two axes. Is my understanding correct? Please let me know if it is, or share your strategy when you have a chance. Thank you very much.

Looking forward your response, Jianming

From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Sunday, February 23, 2025 10:44 AM To: junjie han <hanjunjie2014@gmail.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: Measure angle between domains in chimeraX Hi Junjie, In general there are two ways:

(1) use Define Axes/Planes/Centroids tool or "define" command to define axis or plane objects based on specified atoms. Then you can get the crossing angles between any pairs of these objects using the Axes/Planes/Centroids GUI or the "angle" command. See the following for details: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/axesplanes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html>

(2) if the two domains are structurally similar to each other, you could open two copies of the structure and fit one onto the other, superimposing the parts you want to superimpose (using whatever method you want, "align" or "matchmaker" or manual movements). Then you can get the relationship between the two models with "measure rotation" -- see the following for details: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Feb 22, 2025, at 8:39 PM, junjie han <hanjunjie2014@gmail.com> wrote:

Hi Elaine,

I hope this email finds you well. May I ask how to measure the angle between two domains from one molecule or two different molecules in ChimeraX. Here are some examples below. Example 1:

<image.png>How to calculate these angles (54°, 38°)？

Example 2:<image.png>How to calculate this angle (75°) ?

Example 3:<image.png>How can I measure the rotation angle between A and B, or between two specific regions of these two molecules in ChimeraX? If I need to calculate the rotation angles of two molecules relative to a specific molecule, how can I define a shared axis for calculating the rotation angles? The rotation axes are different when I use the command “measure rotation A toModel B” to calculate the rotation angles, which is not an ideal way to compare them in parallel.

Thank you in advance for your any suggestions.

Very appreciated, Junjie

_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

Hi Elaine, Thank you. My understanding is that the 3D vector of v1 starts from the coordinate (0, 0, 0), which is why I define the axis by connecting coordinate (0,0,0) to the coordinate (-0.508,-0.554,0.659). If not so, is there a way to measure the angle between two 3D vectors in ChimeraX? Best, Junjie ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, February 24, 2025 1:39 PM To: junjie han <hanjunjie2014@gmail.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: Measure angle between domains in chimeraX Hi Junjie, All I can say is what it already says in the help page:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/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. The moments r1, r2, and r3 are calculated as (inertia/mass)½ about axes v1, v2, and v3, respectively. " Aren't 3D vectors always given as 3 numbers? It is the standard way of expressing a vector. See also the standard definition of principal axis. Also I cannot answer whether it divides a subunit into two equal parts. You would need a plane to divide a 3D object, not an axis. Also the object would need to be perfectly symmetric around that plane, which is not likely for a lumpy molecule. Elaine

On Feb 24, 2025, at 10:26 AM, junjie han <hanjunjie2014@gmail.com> wrote:

Hi Elaine,

Thank you.

Could you please help to confirm that whether the v1 vector represents the direction of the axis defined based on the two coordinates (0,0,0) and ( -0.508,-0.554, 0.659) for the subunit A? If so, is the defined axis parallel to the direction of the black line that divides subunit A into two equal parts?

measure inertia #1/A showEllipsoid true Inertia axes for 8dzs, 2074 atoms v1 = -0.508 -0.554 0.659 a = 36.027 r1 = 12.001 v2 = 0.356 -0.832 -0.425 b = 19.480 r2 = 18.103 v3 = 0.784 0.019 0.620 c = 18.455 r3 = 18.316 center = 125.9 126.14 150.23<image.png>Please let me know when you have a chance.

Very appreciated, Junjie

From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, February 24, 2025 10:34 AM To: junjie han <hanjunjie2014@gmail.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: Measure angle between domains in chimeraX You could just use "define axis" with "massWeighting true" -- as far as I know, it should give the same principal axis as "measure inertia" for the same set of atoms.

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#inertia> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#axis>

Both commands take specified atoms, so they are equally "biased," if by biased you mean based on the atoms you specified. You can specify all atoms in the model if that's what you want, but it would really include everything like waters, ligand, etc.

The "measure inertia" help explains the output (v1, v2, v3 etc.) and yes the first one is the longest one. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#inertia>

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Feb 23, 2025, at 2:46 PM, junjie han <hanjunjie2014@gmail.com> wrote:

Hi Elaine,

Thanks for your great response. It is really helpful. Could I ask more questions? Based on your direction, I already figured out how to define the axes and planes and then use 'angle' command to measure the angles between them. However, it may induce a bit of a bias by defining the axes manually. Could the ChimeraX generate a more accurate axis automatically that is through the mass center of the molecule? For instance, the command 'measure inertia #1/A showEllipsoid true' can generate the ellipsoid that is oriented based on the principal axes of inertia. I assume that the principal axis of inertia is through the mass center of the molecule.<image.png>What I need is to generate axes like the black and red lines that go through the center of mass of the molecule and divide it into two equal parts. So how do I get this?

Below is the output after I ran the command 'measure inertia' to show the ellipsoid of two subunits of a complex.

measure inertia #1/A showEllipsoid true Inertia axes for 8dzs, 2074 atoms v1 = -0.508 -0.554 0.659 a = 36.027 r1 = 12.001 v2 = 0.356 -0.832 -0.425 b = 19.480 r2 = 18.103 v3 = 0.784 0.019 0.620 c = 18.455 r3 = 18.316 center = 125.9 126.14 150.23

measure inertia #1/b showEllipsoid true Inertia axes for 8dzs, 1641 atoms v1 = 0.520 0.842 0.141 a = 39.590 r1 = 11.344 v2 = -0.329 0.045 0.943 b = 18.123 r2 = 19.403 v3 = 0.788 -0.537 0.301 c = 17.747 r3 = 19.472 center = 148.04 146.61 117.1

The output shows three vectors, v1, v2, and v3 and the mass center of the subunit. My question is whether the v1 vector represents the direction of the black line of subunit A. If it is, I can define the axis based on the two coordinates (0,0,0) and ( -0.508,-0.554, 0.659) for unit A, and the coordinates (0,0,0) and ( 0.520,0.842, 0.141) for subunit B. After this, I can use the command 'angle' to calculate the angles between two axes. Is my understanding correct? Please let me know if it is, or share your strategy when you have a chance. Thank you very much.

Looking forward your response, Jianming

From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Sunday, February 23, 2025 10:44 AM To: junjie han <hanjunjie2014@gmail.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: Measure angle between domains in chimeraX Hi Junjie, In general there are two ways:

(1) use Define Axes/Planes/Centroids tool or "define" command to define axis or plane objects based on specified atoms. Then you can get the crossing angles between any pairs of these objects using the Axes/Planes/Centroids GUI or the "angle" command. See the following for details: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/axesplanes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html>

(2) if the two domains are structurally similar to each other, you could open two copies of the structure and fit one onto the other, superimposing the parts you want to superimpose (using whatever method you want, "align" or "matchmaker" or manual movements). Then you can get the relationship between the two models with "measure rotation" -- see the following for details: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Feb 22, 2025, at 8:39 PM, junjie han <hanjunjie2014@gmail.com> wrote:

Hi Elaine,

I hope this email finds you well. May I ask how to measure the angle between two domains from one molecule or two different molecules in ChimeraX. Here are some examples below. Example 1:

<image.png>How to calculate these angles (54°, 38°)？

Example 2:<image.png>How to calculate this angle (75°) ?

Example 3:<image.png>How can I measure the rotation angle between A and B, or between two specific regions of these two molecules in ChimeraX? If I need to calculate the rotation angles of two molecules relative to a specific molecule, how can I define a shared axis for calculating the rotation angles? The rotation axes are different when I use the command “measure rotation A toModel B” to calculate the rotation angles, which is not an ideal way to compare them in parallel.

Thank you in advance for your any suggestions.

Very appreciated, Junjie

Hi Elaine, I am not sure which two atoms can be used to define the axis to represent the longest axis of a specific subunit. That's why I do it in a little bit complicated way. Thank you, Junjie ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, February 24, 2025 2:18 PM To: junjie han <hanjunjie2014@gmail.com> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: Measure angle between domains in chimeraX Why don't you just use "define axis" with "massWeighting true" to get the same axis directly (if you specify the same atoms) instead of two steps with "measure inertia"? Elaine

On Feb 24, 2025, at 11:57 AM, junjie han <hanjunjie2014@gmail.com> wrote:

Hi Elaine,

Thank you. My understanding is that the 3D vector of v1 starts from the coordinate (0, 0, 0), which is why I define the axis by connecting coordinate (0,0,0) to the coordinate (-0.508,-0.554,0.659). If not so, is there a way to measure the angle between two 3D vectors in ChimeraX?

Best, Junjie From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, February 24, 2025 1:39 PM To: junjie han <hanjunjie2014@gmail.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: Measure angle between domains in chimeraX Hi Junjie, All I can say is what it already says in the help page:

...

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/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. The moments r1, r2, and r3 are calculated as (inertia/mass)½ about axes v1, v2, and v3, respectively. "

Aren't 3D vectors always given as 3 numbers? It is the standard way of expressing a vector. See also the standard definition of principal axis.

Also I cannot answer whether it divides a subunit into two equal parts. You would need a plane to divide a 3D object, not an axis. Also the object would need to be perfectly symmetric around that plane, which is not likely for a lumpy molecule.

Elaine

...

On Feb 24, 2025, at 10:26 AM, junjie han <hanjunjie2014@gmail.com> wrote:

Hi Elaine,

Thank you.

Could you please help to confirm that whether the v1 vector represents the direction of the axis defined based on the two coordinates (0,0,0) and ( -0.508,-0.554, 0.659) for the subunit A? If so, is the defined axis parallel to the direction of the black line that divides subunit A into two equal parts?

measure inertia #1/A showEllipsoid true Inertia axes for 8dzs, 2074 atoms v1 = -0.508 -0.554 0.659 a = 36.027 r1 = 12.001 v2 = 0.356 -0.832 -0.425 b = 19.480 r2 = 18.103 v3 = 0.784 0.019 0.620 c = 18.455 r3 = 18.316 center = 125.9 126.14 150.23<image.png>Please let me know when you have a chance.

Very appreciated, Junjie

From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, February 24, 2025 10:34 AM To: junjie han <hanjunjie2014@gmail.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: Measure angle between domains in chimeraX You could just use "define axis" with "massWeighting true" -- as far as I know, it should give the same principal axis as "measure inertia" for the same set of atoms.

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#inertia> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#axis>

Both commands take specified atoms, so they are equally "biased," if by biased you mean based on the atoms you specified. You can specify all atoms in the model if that's what you want, but it would really include everything like waters, ligand, etc.

The "measure inertia" help explains the output (v1, v2, v3 etc.) and yes the first one is the longest one. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#inertia>

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Feb 23, 2025, at 2:46 PM, junjie han <hanjunjie2014@gmail.com> wrote:

Hi Elaine,

Thanks for your great response. It is really helpful. Could I ask more questions? Based on your direction, I already figured out how to define the axes and planes and then use 'angle' command to measure the angles between them. However, it may induce a bit of a bias by defining the axes manually. Could the ChimeraX generate a more accurate axis automatically that is through the mass center of the molecule? For instance, the command 'measure inertia #1/A showEllipsoid true' can generate the ellipsoid that is oriented based on the principal axes of inertia. I assume that the principal axis of inertia is through the mass center of the molecule.<image.png>What I need is to generate axes like the black and red lines that go through the center of mass of the molecule and divide it into two equal parts. So how do I get this?

Below is the output after I ran the command 'measure inertia' to show the ellipsoid of two subunits of a complex.

measure inertia #1/A showEllipsoid true Inertia axes for 8dzs, 2074 atoms v1 = -0.508 -0.554 0.659 a = 36.027 r1 = 12.001 v2 = 0.356 -0.832 -0.425 b = 19.480 r2 = 18.103 v3 = 0.784 0.019 0.620 c = 18.455 r3 = 18.316 center = 125.9 126.14 150.23

measure inertia #1/b showEllipsoid true Inertia axes for 8dzs, 1641 atoms v1 = 0.520 0.842 0.141 a = 39.590 r1 = 11.344 v2 = -0.329 0.045 0.943 b = 18.123 r2 = 19.403 v3 = 0.788 -0.537 0.301 c = 17.747 r3 = 19.472 center = 148.04 146.61 117.1

The output shows three vectors, v1, v2, and v3 and the mass center of the subunit. My question is whether the v1 vector represents the direction of the black line of subunit A. If it is, I can define the axis based on the two coordinates (0,0,0) and ( -0.508,-0.554, 0.659) for unit A, and the coordinates (0,0,0) and ( 0.520,0.842, 0.141) for subunit B. After this, I can use the command 'angle' to calculate the angles between two axes. Is my understanding correct? Please let me know if it is, or share your strategy when you have a chance. Thank you very much.

Looking forward your response, Jianming

From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Sunday, February 23, 2025 10:44 AM To: junjie han <hanjunjie2014@gmail.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: Measure angle between domains in chimeraX Hi Junjie, In general there are two ways:

(1) use Define Axes/Planes/Centroids tool or "define" command to define axis or plane objects based on specified atoms. Then you can get the crossing angles between any pairs of these objects using the Axes/Planes/Centroids GUI or the "angle" command. See the following for details: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/axesplanes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html>

(2) if the two domains are structurally similar to each other, you could open two copies of the structure and fit one onto the other, superimposing the parts you want to superimpose (using whatever method you want, "align" or "matchmaker" or manual movements). Then you can get the relationship between the two models with "measure rotation" -- see the following for details: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Feb 22, 2025, at 8:39 PM, junjie han <hanjunjie2014@gmail.com> wrote:

Hi Elaine,

I hope this email finds you well. May I ask how to measure the angle between two domains from one molecule or two different molecules in ChimeraX. Here are some examples below. Example 1:

<image.png>How to calculate these angles (54°, 38°)？

Example 2:<image.png>How to calculate this angle (75°) ?

Example 3:<image.png>How can I measure the rotation angle between A and B, or between two specific regions of these two molecules in ChimeraX? If I need to calculate the rotation angles of two molecules relative to a specific molecule, how can I define a shared axis for calculating the rotation angles? The rotation axes are different when I use the command “measure rotation A toModel B” to calculate the rotation angles, which is not an ideal way to compare them in parallel.

Thank you in advance for your any suggestions.

Very appreciated, Junjie

Hi Junjie, For atomspec purposes, using "define axis" is exactly the same as using "measure inertia" --- it doesn't require only 2 atoms, you can give an atomspec that is the whole model (or whatever set of atoms or residues you used for "measure inertia"). This is explained in the help links I sent before. Elaine

On Feb 24, 2025, at 12:56 PM, junjie han via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Elaine,

I am not sure which two atoms can be used to define the axis to represent the longest axis of a specific subunit. That's why I do it in a little bit complicated way.

Thank you, Junjie From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, February 24, 2025 2:18 PM To: junjie han <hanjunjie2014@gmail.com> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: Measure angle between domains in chimeraX Why don't you just use "define axis" with "massWeighting true" to get the same axis directly (if you specify the same atoms) instead of two steps with "measure inertia"?

Elaine

...

On Feb 24, 2025, at 11:57 AM, junjie han <hanjunjie2014@gmail.com> wrote:

Hi Elaine,

Thank you. My understanding is that the 3D vector of v1 starts from the coordinate (0, 0, 0), which is why I define the axis by connecting coordinate (0,0,0) to the coordinate (-0.508,-0.554,0.659). If not so, is there a way to measure the angle between two 3D vectors in ChimeraX?

Best, Junjie From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, February 24, 2025 1:39 PM To: junjie han <hanjunjie2014@gmail.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: Measure angle between domains in chimeraX Hi Junjie, All I can say is what it already says in the help page:

...

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/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. The moments r1, r2, and r3 are calculated as (inertia/mass)½ about axes v1, v2, and v3, respectively. "

Aren't 3D vectors always given as 3 numbers? It is the standard way of expressing a vector. See also the standard definition of principal axis.

Also I cannot answer whether it divides a subunit into two equal parts. You would need a plane to divide a 3D object, not an axis. Also the object would need to be perfectly symmetric around that plane, which is not likely for a lumpy molecule.

Elaine

...

On Feb 24, 2025, at 10:26 AM, junjie han <hanjunjie2014@gmail.com> wrote:

Hi Elaine,

Thank you.

Could you please help to confirm that whether the v1 vector represents the direction of the axis defined based on the two coordinates (0,0,0) and ( -0.508,-0.554, 0.659) for the subunit A? If so, is the defined axis parallel to the direction of the black line that divides subunit A into two equal parts?

measure inertia #1/A showEllipsoid true Inertia axes for 8dzs, 2074 atoms v1 = -0.508 -0.554 0.659 a = 36.027 r1 = 12.001 v2 = 0.356 -0.832 -0.425 b = 19.480 r2 = 18.103 v3 = 0.784 0.019 0.620 c = 18.455 r3 = 18.316 center = 125.9 126.14 150.23<image.png>Please let me know when you have a chance.

Very appreciated, Junjie

From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, February 24, 2025 10:34 AM To: junjie han <hanjunjie2014@gmail.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: Measure angle between domains in chimeraX You could just use "define axis" with "massWeighting true" -- as far as I know, it should give the same principal axis as "measure inertia" for the same set of atoms.

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#inertia> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#axis>

Both commands take specified atoms, so they are equally "biased," if by biased you mean based on the atoms you specified. You can specify all atoms in the model if that's what you want, but it would really include everything like waters, ligand, etc.

The "measure inertia" help explains the output (v1, v2, v3 etc.) and yes the first one is the longest one. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#inertia>

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Feb 23, 2025, at 2:46 PM, junjie han <hanjunjie2014@gmail.com> wrote:

Hi Elaine,

Thanks for your great response. It is really helpful. Could I ask more questions? Based on your direction, I already figured out how to define the axes and planes and then use 'angle' command to measure the angles between them. However, it may induce a bit of a bias by defining the axes manually. Could the ChimeraX generate a more accurate axis automatically that is through the mass center of the molecule? For instance, the command 'measure inertia #1/A showEllipsoid true' can generate the ellipsoid that is oriented based on the principal axes of inertia. I assume that the principal axis of inertia is through the mass center of the molecule.<image.png>What I need is to generate axes like the black and red lines that go through the center of mass of the molecule and divide it into two equal parts. So how do I get this?

Below is the output after I ran the command 'measure inertia' to show the ellipsoid of two subunits of a complex.

measure inertia #1/A showEllipsoid true Inertia axes for 8dzs, 2074 atoms v1 = -0.508 -0.554 0.659 a = 36.027 r1 = 12.001 v2 = 0.356 -0.832 -0.425 b = 19.480 r2 = 18.103 v3 = 0.784 0.019 0.620 c = 18.455 r3 = 18.316 center = 125.9 126.14 150.23

measure inertia #1/b showEllipsoid true Inertia axes for 8dzs, 1641 atoms v1 = 0.520 0.842 0.141 a = 39.590 r1 = 11.344 v2 = -0.329 0.045 0.943 b = 18.123 r2 = 19.403 v3 = 0.788 -0.537 0.301 c = 17.747 r3 = 19.472 center = 148.04 146.61 117.1

The output shows three vectors, v1, v2, and v3 and the mass center of the subunit. My question is whether the v1 vector represents the direction of the black line of subunit A. If it is, I can define the axis based on the two coordinates (0,0,0) and ( -0.508,-0.554, 0.659) for unit A, and the coordinates (0,0,0) and ( 0.520,0.842, 0.141) for subunit B. After this, I can use the command 'angle' to calculate the angles between two axes. Is my understanding correct? Please let me know if it is, or share your strategy when you have a chance. Thank you very much.

Looking forward your response, Jianming

From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Sunday, February 23, 2025 10:44 AM To: junjie han <hanjunjie2014@gmail.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: Measure angle between domains in chimeraX Hi Junjie, In general there are two ways:

(1) use Define Axes/Planes/Centroids tool or "define" command to define axis or plane objects based on specified atoms. Then you can get the crossing angles between any pairs of these objects using the Axes/Planes/Centroids GUI or the "angle" command. See the following for details: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/axesplanes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html>

(2) if the two domains are structurally similar to each other, you could open two copies of the structure and fit one onto the other, superimposing the parts you want to superimpose (using whatever method you want, "align" or "matchmaker" or manual movements). Then you can get the relationship between the two models with "measure rotation" -- see the following for details: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Feb 22, 2025, at 8:39 PM, junjie han <hanjunjie2014@gmail.com> wrote:

Hi Elaine,

I hope this email finds you well. May I ask how to measure the angle between two domains from one molecule or two different molecules in ChimeraX. Here are some examples below. Example 1:

<image.png>How to calculate these angles (54°, 38°)？

Example 2:<image.png>How to calculate this angle (75°) ?

Example 3:<image.png>How can I measure the rotation angle between A and B, or between two specific regions of these two molecules in ChimeraX? If I need to calculate the rotation angles of two molecules relative to a specific molecule, how can I define a shared axis for calculating the rotation angles? The rotation axes are different when I use the command “measure rotation A toModel B” to calculate the rotation angles, which is not an ideal way to compare them in parallel.

Thank you in advance for your any suggestions.

Very appreciated, Junjie

_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

Thank you so much. This makes my job easy. Best, Jianming ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Monday, February 24, 2025 3:47 PM To: junjie han <hanjunjie2014@gmail.com> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Measure angle between domains in chimeraX Hi Junjie, You specify all the atoms with the define axis command, not just two atoms. Just like measure inertia it does a fit to all the atoms you specify open 1fav define axis /C massWeighting trueAxis

'1fav #1/axis' centered at [13.55662713 0.25199894 51.94656556] with direction [ 0.39755183 -0.14200389 -0.90652492], radius 3.55232, and length 50.9477

measure inertia /CInertia axes for 1fav, 260 atoms

v1 = -0.396 0.142 0.907 a = 31.092 r1 = 3.961 v2 = -0.173 -0.982 0.078 b = 6.662 r2 = 14.147 v3 = 0.902 -0.126 0.413 c = 5.836 r3 = 14.220 center = 13.796 0.1666 51.401

Tom On Feb 24, 2025, at 12:56 PM, junjie han via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hi Elaine, I am not sure which two atoms can be used to define the axis to represent the longest axis of a specific subunit. That's why I do it in a little bit complicated way. Thank you, Junjie ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> Sent: Monday, February 24, 2025 2:18 PM To: junjie han <hanjunjie2014@gmail.com<mailto:hanjunjie2014@gmail.com>> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: Measure angle between domains in chimeraX Why don't you just use "define axis" with "massWeighting true" to get the same axis directly (if you specify the same atoms) instead of two steps with "measure inertia"? Elaine

On Feb 24, 2025, at 11:57 AM, junjie han <hanjunjie2014@gmail.com<mailto:hanjunjie2014@gmail.com>> wrote:

Hi Elaine,

Thank you. My understanding is that the 3D vector of v1 starts from the coordinate (0, 0, 0), which is why I define the axis by connecting coordinate (0,0,0) to the coordinate (-0.508,-0.554,0.659). If not so, is there a way to measure the angle between two 3D vectors in ChimeraX?

Best, Junjie From: Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> Sent: Monday, February 24, 2025 1:39 PM To: junjie han <hanjunjie2014@gmail.com<mailto:hanjunjie2014@gmail.com>> Cc: chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: Measure angle between domains in chimeraX Hi Junjie, All I can say is what it already says in the help page:

...

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/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. The moments r1, r2, and r3 are calculated as (inertia/mass)½ about axes v1, v2, and v3, respectively. "

Aren't 3D vectors always given as 3 numbers? It is the standard way of expressing a vector. See also the standard definition of principal axis.

Also I cannot answer whether it divides a subunit into two equal parts. You would need a plane to divide a 3D object, not an axis. Also the object would need to be perfectly symmetric around that plane, which is not likely for a lumpy molecule.

Elaine

...

On Feb 24, 2025, at 10:26 AM, junjie han <hanjunjie2014@gmail.com<mailto:hanjunjie2014@gmail.com>> wrote:

Hi Elaine,

Thank you.

Could you please help to confirm that whether the v1 vector represents the direction of the axis defined based on the two coordinates (0,0,0) and ( -0.508,-0.554, 0.659) for the subunit A? If so, is the defined axis parallel to the direction of the black line that divides subunit A into two equal parts?

measure inertia #1/A showEllipsoid true Inertia axes for 8dzs, 2074 atoms v1 = -0.508 -0.554 0.659 a = 36.027 r1 = 12.001 v2 = 0.356 -0.832 -0.425 b = 19.480 r2 = 18.103 v3 = 0.784 0.019 0.620 c = 18.455 r3 = 18.316 center = 125.9 126.14 150.23<image.png>Please let me know when you have a chance.

Very appreciated, Junjie

From: Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> Sent: Monday, February 24, 2025 10:34 AM To: junjie han <hanjunjie2014@gmail.com<mailto:hanjunjie2014@gmail.com>> Cc: chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: Measure angle between domains in chimeraX You could just use "define axis" with "massWeighting true" -- as far as I know, it should give the same principal axis as "measure inertia" for the same set of atoms.

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#inertia> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#axis>

Both commands take specified atoms, so they are equally "biased," if by biased you mean based on the atoms you specified. You can specify all atoms in the model if that's what you want, but it would really include everything like waters, ligand, etc.

The "measure inertia" help explains the output (v1, v2, v3 etc.) and yes the first one is the longest one. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#inertia>

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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On Feb 23, 2025, at 2:46 PM, junjie han <hanjunjie2014@gmail.com<mailto:hanjunjie2014@gmail.com>> wrote:

Hi Elaine,

Thanks for your great response. It is really helpful. Could I ask more questions? Based on your direction, I already figured out how to define the axes and planes and then use 'angle' command to measure the angles between them. However, it may induce a bit of a bias by defining the axes manually. Could the ChimeraX generate a more accurate axis automatically that is through the mass center of the molecule? For instance, the command 'measure inertia #1/A showEllipsoid true' can generate the ellipsoid that is oriented based on the principal axes of inertia. I assume that the principal axis of inertia is through the mass center of the molecule.<image.png>What I need is to generate axes like the black and red lines that go through the center of mass of the molecule and divide it into two equal parts. So how do I get this?

Below is the output after I ran the command 'measure inertia' to show the ellipsoid of two subunits of a complex.

measure inertia #1/A showEllipsoid true Inertia axes for 8dzs, 2074 atoms v1 = -0.508 -0.554 0.659 a = 36.027 r1 = 12.001 v2 = 0.356 -0.832 -0.425 b = 19.480 r2 = 18.103 v3 = 0.784 0.019 0.620 c = 18.455 r3 = 18.316 center = 125.9 126.14 150.23

measure inertia #1/b showEllipsoid true Inertia axes for 8dzs, 1641 atoms v1 = 0.520 0.842 0.141 a = 39.590 r1 = 11.344 v2 = -0.329 0.045 0.943 b = 18.123 r2 = 19.403 v3 = 0.788 -0.537 0.301 c = 17.747 r3 = 19.472 center = 148.04 146.61 117.1

The output shows three vectors, v1, v2, and v3 and the mass center of the subunit. My question is whether the v1 vector represents the direction of the black line of subunit A. If it is, I can define the axis based on the two coordinates (0,0,0) and ( -0.508,-0.554, 0.659) for unit A, and the coordinates (0,0,0) and ( 0.520,0.842, 0.141) for subunit B. After this, I can use the command 'angle' to calculate the angles between two axes. Is my understanding correct? Please let me know if it is, or share your strategy when you have a chance. Thank you very much.

Looking forward your response, Jianming

From: Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> Sent: Sunday, February 23, 2025 10:44 AM To: junjie han <hanjunjie2014@gmail.com<mailto:hanjunjie2014@gmail.com>> Cc: chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: Measure angle between domains in chimeraX Hi Junjie, In general there are two ways:

(1) use Define Axes/Planes/Centroids tool or "define" command to define axis or plane objects based on specified atoms. Then you can get the crossing angles between any pairs of these objects using the Axes/Planes/Centroids GUI or the "angle" command. See the following for details: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/axesplanes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html>

(2) if the two domains are structurally similar to each other, you could open two copies of the structure and fit one onto the other, superimposing the parts you want to superimpose (using whatever method you want, "align" or "matchmaker" or manual movements). Then you can get the relationship between the two models with "measure rotation" -- see the following for details: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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On Feb 22, 2025, at 8:39 PM, junjie han <hanjunjie2014@gmail.com<mailto:hanjunjie2014@gmail.com>> wrote:

Hi Elaine,

I hope this email finds you well. May I ask how to measure the angle between two domains from one molecule or two different molecules in ChimeraX. Here are some examples below. Example 1:

<image.png>How to calculate these angles (54°, 38°)？

Example 2:<image.png>How to calculate this angle (75°) ?

Example 3:<image.png>How can I measure the rotation angle between A and B, or between two specific regions of these two molecules in ChimeraX? If I need to calculate the rotation angles of two molecules relative to a specific molecule, how can I define a shared axis for calculating the rotation angles? The rotation axes are different when I use the command “measure rotation A toModel B” to calculate the rotation angles, which is not an ideal way to compare them in parallel.

Thank you in advance for your any suggestions.

Very appreciated, Junjie

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