Request for Mathematical Details or Source Code for Helix Axis and Interhelical Distace/Angle Calculations in Chimera
Respected Sir/Madam, My name is Prashant Upadhyay, and I am currently pursuing a Ph.D. in Bioinformatics and Molecular Dynamics Simulation at the Indian Institute of Technology Kanpur (IIT Kanpur), India. As part of my research, I am analyzing the structural dynamics of helical membrane proteins using molecular dynamics simulations. I have been using UCSF Chimera extensively for structural analysis. Specifically, I have been utilizing the Structure Analysis → Axes/Planes/Centroids tool to calculate the helix axes of selected helices in my protein of interest. When I select two helices, the Reply Log provides the interhelical distance and angle between the computed axes. This functionality has been incredibly useful for analyzing static structures. To extend this to a dynamic context, I am interested in applying the same axis and angle calculation to each frame of an MD trajectory. For this, I would greatly appreciate it if you could share the mathematical methodology or the relevant portion of the source code that Chimera uses to compute: 1)The helix axis from selected residues 2)The angle and the shortest distance between two helix axes My aim is to replicate this analysis programmatically over the entire simulation trajectory. Any guidance, reference, or code snippet you could provide would be immensely helpful. Thank you, Prashant Upadhyay Ph.D. Student Department of Biological Sciences and Bioengineering Indian Institute of Technology Kanpur (IIT Kanpur)
Hello Prashant, If you can play back the trajectory in Chimera (MD Movie tool) or ChimeraX (coordset command) it may be easier just to run the analysis in the program. If you are asking only for Chimera you should use the chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> address, if for ChimeraX you should use the chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address. You sent it to both addresses, but your question only mentioned Chimera, so I don't know if you are willing to use ChimeraX. However, I will try to answer generally. To do the whole calculation in Chimera or ChimeraX: (1) figure out the commands you want to run on each trajectory frame, e.g. "define" to create the axes, "angle" to measure angle and "distance" to measure distance, "close" to close the axis models from that frame. The commands would be slightly different for Chimera vs. ChimeraX. You would figure the commands out by showing one trajectory frame and simply entering the commands until you get it right. This process of trial and error may take you a while but is important. (2) then there is a way to run this set of commands at every trajectory frame as you play the trajectory back In Chimera the MD Movie tool has its own menu with Per-Frame... Define Script where you can enter the commands to be executed at each trajectory frame, see <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie....> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#...> ChimeraX does not have that GUI, but you can do it with the "perframe" command to set up the script to run every frame and the "coordset" command to play back the trajectory, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html> <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> 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 Jun 22, 2025, at 5:19 AM, pupadhyay21 via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Respected Sir/Madam, My name is Prashant Upadhyay, and I am currently pursuing a Ph.D. in Bioinformatics and Molecular Dynamics Simulation at the Indian Institute of Technology Kanpur (IIT Kanpur), India. As part of my research, I am analyzing the structural dynamics of helical membrane proteins using molecular dynamics simulations.
I have been using UCSF Chimera extensively for structural analysis. Specifically, I have been utilizing the Structure Analysis → Axes/Planes/Centroids tool to calculate the helix axes of selected helices in my protein of interest. When I select two helices, the Reply Log provides the interhelical distance and angle between the computed axes. This functionality has been incredibly useful for analyzing static structures.
To extend this to a dynamic context, I am interested in applying the same axis and angle calculation to each frame of an MD trajectory. For this, I would greatly appreciate it if you could share the mathematical methodology or the relevant portion of the source code that Chimera uses to compute: 1)The helix axis from selected residues 2)The angle and the shortest distance between two helix axes
My aim is to replicate this analysis programmatically over the entire simulation trajectory. Any guidance, reference, or code snippet you could provide would be immensely helpful.
Thank you, Prashant Upadhyay Ph.D. Student Department of Biological Sciences and Bioengineering Indian Institute of Technology Kanpur (IIT Kanpur) _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
Hi Prashant, Elaine did an excellent job showing how you can get Chimera/ChimeraX to compute those values for you. You also asked about the methodology of how the values are computed. Here is the relevant code sections (from ChimeraX, since it’s easier to reference its code since it’s in GitHub). compute axis: https://github.com/RBVI/ChimeraX/blob/176571d15a9dce874ce67e2d14b9cb942ccc60... crossing angle: https://github.com/RBVI/ChimeraX/blob/176571d15a9dce874ce67e2d14b9cb942ccc60... and https://github.com/RBVI/ChimeraX/blob/176571d15a9dce874ce67e2d14b9cb942ccc60... crossing distance: https://github.com/RBVI/ChimeraX/blob/176571d15a9dce874ce67e2d14b9cb942ccc60... --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jun 23, 2025, at 9:53 AM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello Prashant, If you can play back the trajectory in Chimera (MD Movie tool) or ChimeraX (coordset command) it may be easier just to run the analysis in the program. If you are asking only for Chimera you should use the chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu><mailto:chimera-users@cgl.ucsf.edu> address, if for ChimeraX you should use the chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu><mailto:chimerax-users@cgl.ucsf.edu> address. You sent it to both addresses, but your question only mentioned Chimera, so I don't know if you are willing to use ChimeraX. However, I will try to answer generally.
To do the whole calculation in Chimera or ChimeraX:
(1) figure out the commands you want to run on each trajectory frame, e.g. "define" to create the axes, "angle" to measure angle and "distance" to measure distance, "close" to close the axis models from that frame. The commands would be slightly different for Chimera vs. ChimeraX. You would figure the commands out by showing one trajectory frame and simply entering the commands until you get it right. This process of trial and error may take you a while but is important.
(2) then there is a way to run this set of commands at every trajectory frame as you play the trajectory back
In Chimera the MD Movie tool has its own menu with Per-Frame... Define Script where you can enter the commands to be executed at each trajectory frame, see <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie....> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#...>
ChimeraX does not have that GUI, but you can do it with the "perframe" command to set up the script to run every frame and the "coordset" command to play back the trajectory, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html> <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
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 Jun 22, 2025, at 5:19 AM, pupadhyay21 via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote:
Respected Sir/Madam, My name is Prashant Upadhyay, and I am currently pursuing a Ph.D. in Bioinformatics and Molecular Dynamics Simulation at the Indian Institute of Technology Kanpur (IIT Kanpur), India. As part of my research, I am analyzing the structural dynamics of helical membrane proteins using molecular dynamics simulations.
I have been using UCSF Chimera extensively for structural analysis. Specifically, I have been utilizing the Structure Analysis → Axes/Planes/Centroids tool to calculate the helix axes of selected helices in my protein of interest. When I select two helices, the Reply Log provides the interhelical distance and angle between the computed axes. This functionality has been incredibly useful for analyzing static structures.
To extend this to a dynamic context, I am interested in applying the same axis and angle calculation to each frame of an MD trajectory. For this, I would greatly appreciate it if you could share the mathematical methodology or the relevant portion of the source code that Chimera uses to compute: 1)The helix axis from selected residues 2)The angle and the shortest distance between two helix axes
My aim is to replicate this analysis programmatically over the entire simulation trajectory. Any guidance, reference, or code snippet you could provide would be immensely helpful.
Thank you, Prashant Upadhyay Ph.D. Student Department of Biological Sciences and Bioengineering Indian Institute of Technology Kanpur (IIT Kanpur) _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu <mailto:chimera-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
_______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu <mailto:chimera-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
Hi Eric and Elaine, Thank you both very much for your detailed and prompt responses. Elaine, your explanation on how to perform per-frame analysis in both Chimera and ChimeraX was incredibly helpful and clarified many of my doubts regarding the implementation side of things. Eric, thank you for sharing the specific code references from the ChimeraX GitHub repository. This is exactly what I needed to understand the underlying mathematical approach. Due to hardware limitations, I have to work on a very old PC without a graphics card, loading large protein trajectories in Chimera or ChimeraX is practically infeasible, often causing my system to freeze. This is why I was looking to replicate the analysis programmatically. Warm regards, Prashant Upadhyay Ph.D. Student Department of Biological Sciences and Bioengineering Indian Institute of Technology Kanpur On 2025-06-24 02:19, Eric Pettersen wrote:
Hi Prashant, Elaine did an excellent job showing how you can get Chimera/ChimeraX to compute those values for you. You also asked about the methodology of how the values are computed. Here is the relevant code sections (from ChimeraX, since it’s easier to reference its code since it’s in GitHub).
compute axis:
https://github.com/RBVI/ChimeraX/blob/176571d15a9dce874ce67e2d14b9cb942ccc60...
crossing angle:
https://github.com/RBVI/ChimeraX/blob/176571d15a9dce874ce67e2d14b9cb942ccc60...
and
https://github.com/RBVI/ChimeraX/blob/176571d15a9dce874ce67e2d14b9cb942ccc60...
crossing distance:
https://github.com/RBVI/ChimeraX/blob/176571d15a9dce874ce67e2d14b9cb942ccc60...
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 23, 2025, at 9:53 AM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote: Hello Prashant, If you can play back the trajectory in Chimera (MD Movie tool) or ChimeraX (coordset command) it may be easier just to run the analysis in the program. If you are asking only for Chimera you should use the chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> address, if for ChimeraX you should use the chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> address. You sent it to both addresses, but your question only mentioned Chimera, so I don't know if you are willing to use ChimeraX. However, I will try to answer generally.
To do the whole calculation in Chimera or ChimeraX:
(1) figure out the commands you want to run on each trajectory frame, e.g. "define" to create the axes, "angle" to measure angle and "distance" to measure distance, "close" to close the axis models from that frame. The commands would be slightly different for Chimera vs. ChimeraX. You would figure the commands out by showing one trajectory frame and simply entering the commands until you get it right. This process of trial and error may take you a while but is important.
(2) then there is a way to run this set of commands at every trajectory frame as you play the trajectory back
In Chimera the MD Movie tool has its own menu with Per-Frame... Define Script where you can enter the commands to be executed at each trajectory frame, see
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie....>
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#...>
ChimeraX does not have that GUI, but you can do it with the "perframe" command to set up the script to run every frame and the "coordset" command to play back the trajectory, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html>
<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
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 Jun 22, 2025, at 5:19 AM, pupadhyay21 via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Respected Sir/Madam, My name is Prashant Upadhyay, and I am currently pursuing a Ph.D. in Bioinformatics and Molecular Dynamics Simulation at the Indian Institute of Technology Kanpur (IIT Kanpur), India. As part of my research, I am analyzing the structural dynamics of helical membrane proteins using molecular dynamics simulations.
I have been using UCSF Chimera extensively for structural analysis. Specifically, I have been utilizing the Structure Analysis → Axes/Planes/Centroids tool to calculate the helix axes of selected helices in my protein of interest. When I select two helices, the Reply Log provides the interhelical distance and angle between the computed axes. This functionality has been incredibly useful for analyzing static structures.
To extend this to a dynamic context, I am interested in applying the same axis and angle calculation to each frame of an MD trajectory. For this, I would greatly appreciate it if you could share the mathematical methodology or the relevant portion of the source code that Chimera uses to compute: 1)The helix axis from selected residues 2)The angle and the shortest distance between two helix axes
My aim is to replicate this analysis programmatically over the entire simulation trajectory. Any guidance, reference, or code snippet you could provide would be immensely helpful.
Thank you, Prashant Upadhyay Ph.D. Student Department of Biological Sciences and Bioengineering Indian Institute of Technology Kanpur (IIT Kanpur) _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives:
https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
_______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives:
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participants (3)
-
Elaine Meng -
Eric Pettersen -
pupadhyay21