Time evolution of the crossing angle between helices during MD trajectories
In Chimera’s Structure Measurement tool, for a given protein, clicking on the Define axes gives the Cartesian coordinates of the centre of each helix as well as its direction. Selecting two helices (say helix 5 and 6) gives the angle and distance between these helices. I take it that the distance is defined as that between the centroids of the centre of mass of the two helices. The question is whether it is possible to work out the time evolution of the crossing angle between to helices during an MD trajectory. MD Movie/Analysis/Plots/Angles plots the angle between three atoms rather than the crossing angle of the chosen helices. Am I right? Missing something? Thanks in advance for your help George
Hi George, What you get from choosing two axes in the "Axes/Planes/Centroids” table is not the distance between their center points, but their closest distance (along the whole axes). You also get the crossing angle. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes> You would need to use MD Movie per-frame scripting, with commands: define axes with the “define” command and measure their crossing angle with the “angle” command. That way you could get a value reported to the Reply Log at each frame. After defining the script, you would need to clear the Reply Log, then go to trajectory frame 1 and run through the whole thing once with looping turned off, then save the results from the Reply Log to a text file for further processing, for example, keeping only the lines with “Angle". (You might have done this before for distances or H-bonds.) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html> You can’t use the MD Movie plotting for this purpose; it only does angle calculations for atoms. The reason is that it is clear which atom is the same atom in different trajectory frames, but it is not clear which axis would be the same axis because you have to recalculate and replace them at each step, and they might be based on different sets of atoms at different steps as residues become more or less helical. If your structure is constant enough that you think it will always have the same set of helices (even though they might change in length and position), then your “define” command could just recalculate all the helix axes in the structure, because then you could rely on the same IDs for the same two helices. In other words if the structure will always have the same 8 helices, a per-frame script with something like the following would allow a valid comparison: ~define axes define axis perHelix true angle a4 a7 However, if there might be more or fewer helices at different frames in the trajectory, your “define” commands would instead need to reference specific residue ranges, which might not always be completely helical. ~define axes define axis :10-18@n,ca,c number 1 define axis :58-66@n,ca,c number 2 angle a1 a2 I tried something similar on an ensemble of 18 conformations, and then the lines with “Angle” from the Reply Log were: Angle between a1 and a2 is 37.793 Angle between a1 and a2 is 20.357 Angle between a1 and a2 is 24.017 Angle between a1 and a2 is 7.086 Angle between a1 and a2 is 57.136 Angle between a1 and a2 is 25.112 Angle between a1 and a2 is 2.874 Angle between a1 and a2 is 22.765 Angle between a1 and a2 is 6.126 Angle between a1 and a2 is 23.888 Angle between a1 and a2 is 84.587 Angle between a1 and a2 is 5.281 Angle between a1 and a2 is 57.247 Angle between a1 and a2 is 50.152 Angle between a1 and a2 is 76.289 Angle between a1 and a2 is 16.187 Angle between a1 and a2 is 22.873 Angle between a1 and a2 is 28.225 You could choose to use different “define” options, like helical correction, etc. 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 27, 2017, at 9:07 AM, George Tzotzos <gtzotzos@me.com> wrote:
In Chimera’s Structure Measurement tool, for a given protein, clicking on the Define axes gives the Cartesian coordinates of the centre of each helix as well as its direction. Selecting two helices (say helix 5 and 6) gives the angle and distance between these helices. I take it that the distance is defined as that between the centroids of the centre of mass of the two helices.
The question is whether it is possible to work out the time evolution of the crossing angle between to helices during an MD trajectory.
MD Movie/Analysis/Plots/Angles plots the angle between three atoms rather than the crossing angle of the chosen helices. Am I right? Missing something?
Thanks in advance for your help
George
Elaine, many thanks for the helpful suggestions. I’m going through my trajectory (30000 frames) and although I set the step to 500 (see attached snapshot), Chimera seems to iterate frame by frame. Is there a way round it? 30000 frames is an overkill. All the best George
On 27 Sep 2017, at 19:58, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi George, What you get from choosing two axes in the "Axes/Planes/Centroids” table is not the distance between their center points, but their closest distance (along the whole axes). You also get the crossing angle. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>
You would need to use MD Movie per-frame scripting, with commands: define axes with the “define” command and measure their crossing angle with the “angle” command. That way you could get a value reported to the Reply Log at each frame. After defining the script, you would need to clear the Reply Log, then go to trajectory frame 1 and run through the whole thing once with looping turned off, then save the results from the Reply Log to a text file for further processing, for example, keeping only the lines with “Angle". (You might have done this before for distances or H-bonds.) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>
You can’t use the MD Movie plotting for this purpose; it only does angle calculations for atoms. The reason is that it is clear which atom is the same atom in different trajectory frames, but it is not clear which axis would be the same axis because you have to recalculate and replace them at each step, and they might be based on different sets of atoms at different steps as residues become more or less helical.
If your structure is constant enough that you think it will always have the same set of helices (even though they might change in length and position), then your “define” command could just recalculate all the helix axes in the structure, because then you could rely on the same IDs for the same two helices. In other words if the structure will always have the same 8 helices, a per-frame script with something like the following would allow a valid comparison:
~define axes define axis perHelix true angle a4 a7
However, if there might be more or fewer helices at different frames in the trajectory, your “define” commands would instead need to reference specific residue ranges, which might not always be completely helical.
~define axes define axis :10-18@n,ca,c number 1 define axis :58-66@n,ca,c number 2 angle a1 a2
I tried something similar on an ensemble of 18 conformations, and then the lines with “Angle” from the Reply Log were: Angle between a1 and a2 is 37.793 Angle between a1 and a2 is 20.357 Angle between a1 and a2 is 24.017 Angle between a1 and a2 is 7.086 Angle between a1 and a2 is 57.136 Angle between a1 and a2 is 25.112 Angle between a1 and a2 is 2.874 Angle between a1 and a2 is 22.765 Angle between a1 and a2 is 6.126 Angle between a1 and a2 is 23.888 Angle between a1 and a2 is 84.587 Angle between a1 and a2 is 5.281 Angle between a1 and a2 is 57.247 Angle between a1 and a2 is 50.152 Angle between a1 and a2 is 76.289 Angle between a1 and a2 is 16.187 Angle between a1 and a2 is 22.873 Angle between a1 and a2 is 28.225
You could choose to use different “define” options, like helical correction, etc. 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 27, 2017, at 9:07 AM, George Tzotzos <gtzotzos@me.com> wrote:
In Chimera’s Structure Measurement tool, for a given protein, clicking on the Define axes gives the Cartesian coordinates of the centre of each helix as well as its direction. Selecting two helices (say helix 5 and 6) gives the angle and distance between these helices. I take it that the distance is defined as that between the centroids of the centre of mass of the two helices.
The question is whether it is possible to work out the time evolution of the crossing angle between to helices during an MD trajectory.
MD Movie/Analysis/Plots/Angles plots the angle between three atoms rather than the crossing angle of the chosen helices. Am I right? Missing something?
Thanks in advance for your help
George
Make sure you hit Return when typing in the step size — otherwise it doesn’t know you’re done typing. —Eric
On Sep 27, 2017, at 12:49 PM, George Tzotzos <gtzotzos@me.com> wrote:
Elaine, many thanks for the helpful suggestions.
I’m going through my trajectory (30000 frames) and although I set the step to 500 (see attached snapshot), Chimera seems to iterate frame by frame. Is there a way round it? 30000 frames is an overkill.
All the best
George
<PastedGraphic-1.png>
On 27 Sep 2017, at 19:58, Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote:
Hi George, What you get from choosing two axes in the "Axes/Planes/Centroids” table is not the distance between their center points, but their closest distance (along the whole axes). You also get the crossing angle. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru... <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>>
You would need to use MD Movie per-frame scripting, with commands: define axes with the “define” command and measure their crossing angle with the “angle” command. That way you could get a value reported to the Reply Log at each frame. After defining the script, you would need to clear the Reply Log, then go to trajectory frame 1 and run through the whole thing once with looping turned off, then save the results from the Reply Log to a text file for further processing, for example, keeping only the lines with “Angle". (You might have done this before for distances or H-bonds.) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>>
You can’t use the MD Movie plotting for this purpose; it only does angle calculations for atoms. The reason is that it is clear which atom is the same atom in different trajectory frames, but it is not clear which axis would be the same axis because you have to recalculate and replace them at each step, and they might be based on different sets of atoms at different steps as residues become more or less helical.
If your structure is constant enough that you think it will always have the same set of helices (even though they might change in length and position), then your “define” command could just recalculate all the helix axes in the structure, because then you could rely on the same IDs for the same two helices. In other words if the structure will always have the same 8 helices, a per-frame script with something like the following would allow a valid comparison:
~define axes define axis perHelix true angle a4 a7
However, if there might be more or fewer helices at different frames in the trajectory, your “define” commands would instead need to reference specific residue ranges, which might not always be completely helical.
~define axes define axis :10-18@n,ca,c number 1 define axis :58-66@n,ca,c number 2 angle a1 a2
I tried something similar on an ensemble of 18 conformations, and then the lines with “Angle” from the Reply Log were: Angle between a1 and a2 is 37.793 Angle between a1 and a2 is 20.357 Angle between a1 and a2 is 24.017 Angle between a1 and a2 is 7.086 Angle between a1 and a2 is 57.136 Angle between a1 and a2 is 25.112 Angle between a1 and a2 is 2.874 Angle between a1 and a2 is 22.765 Angle between a1 and a2 is 6.126 Angle between a1 and a2 is 23.888 Angle between a1 and a2 is 84.587 Angle between a1 and a2 is 5.281 Angle between a1 and a2 is 57.247 Angle between a1 and a2 is 50.152 Angle between a1 and a2 is 76.289 Angle between a1 and a2 is 16.187 Angle between a1 and a2 is 22.873 Angle between a1 and a2 is 28.225
You could choose to use different “define” options, like helical correction, etc. 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 27, 2017, at 9:07 AM, George Tzotzos <gtzotzos@me.com <mailto:gtzotzos@me.com>> wrote:
In Chimera’s Structure Measurement tool, for a given protein, clicking on the Define axes gives the Cartesian coordinates of the centre of each helix as well as its direction. Selecting two helices (say helix 5 and 6) gives the angle and distance between these helices. I take it that the distance is defined as that between the centroids of the centre of mass of the two helices.
The question is whether it is possible to work out the time evolution of the crossing angle between to helices during an MD trajectory.
MD Movie/Analysis/Plots/Angles plots the angle between three atoms rather than the crossing angle of the chosen helices. Am I right? Missing something?
Thanks in advance for your help
George
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participants (3)
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Elaine Meng -
Eric Pettersen -
George Tzotzos