the artifacts of the PBC of the MD trajectory
Dear Chimera-X users ! I am visualizing an MD trajectory of a biomembrane system obtained from Amber MD using the autoimage method of cpptraj. However, in this trajectory, I still observe very rapid lateral diffusion of certain lipids, which cross the entire system too quickly. Is there a way in ChimeraX to hide or suppress such motions for selected atomic groups (e.g., lipids)? Many thanks in advance Enrico
Not really, other than hiding them entirely. Of course you could just make a separate model that contains one frame and have them sit there without moving, but that seems like it would be misleading. 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 Nov 6, 2024, at 11:35 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
I am visualizing an MD trajectory of a biomembrane system obtained from Amber MD using the autoimage method of cpptraj. However, in this trajectory, I still observe very rapid lateral diffusion of certain lipids, which cross the entire system too quickly. Is there a way in ChimeraX to hide or suppress such motions for selected atomic groups (e.g., lipids)?
Many thanks in advance
Enrico
Thank you very much Elaine ! Could we automatically select in Chimera-X all (residues?) lipids that cross the membrane back and forth ? Yours sincerely Enrico Il giorno mer 6 nov 2024 alle ore 22:20 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Not really, other than hiding them entirely.
Of course you could just make a separate model that contains one frame and have them sit there without moving, but that seems like it would be misleading.
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 Nov 6, 2024, at 11:35 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
I am visualizing an MD trajectory of a biomembrane system obtained from Amber MD using the autoimage method of cpptraj. However, in this trajectory, I still observe very rapid lateral diffusion of certain lipids, which cross the entire system too quickly. Is there a way in ChimeraX to hide or suppress such motions for selected atomic groups (e.g., lipids)?
Many thanks in advance
Enrico
There is no way to automatically select what crosses. Of course, if you know their residue numbers and/or residue names you would use the usual way to specify them directly. Elaine
On Nov 7, 2024, at 12:31 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much Elaine !
Could we automatically select in Chimera-X all (residues?) lipids that cross the membrane back and forth ?
Yours sincerely
Enrico
Il giorno mer 6 nov 2024 alle ore 22:20 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: Not really, other than hiding them entirely.
Of course you could just make a separate model that contains one frame and have them sit there without moving, but that seems like it would be misleading.
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 Nov 6, 2024, at 11:35 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
I am visualizing an MD trajectory of a biomembrane system obtained from Amber MD using the autoimage method of cpptraj. However, in this trajectory, I still observe very rapid lateral diffusion of certain lipids, which cross the entire system too quickly. Is there a way in ChimeraX to hide or suppress such motions for selected atomic groups (e.g., lipids)?
Many thanks in advance
Enrico
Thank you very much for this suggestion, Elaine! In the described bilayer system visualization, we’re encountering an issue related to periodic boundary conditions (PBC). Specifically, when lipids cross the boundary, they disappear from one side (e.g., the bottom) and reappear on the opposite side (e.g., the top). While this isn’t particularly noticeable in the default representation, switching to the surface representation of lipids, reveals a significant visual artifact: lipids that cross boundaries appear to jump across the entire box in the lateral direction. It would be great if Eric could help us out here—perhaps with a custom Python solution to clean up the visualization and smooth out the situation. Yours with thanks Enrico Il giorno gio 7 nov 2024 alle ore 17:26 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
There is no way to automatically select what crosses. Of course, if you know their residue numbers and/or residue names you would use the usual way to specify them directly.
Elaine
On Nov 7, 2024, at 12:31 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much Elaine !
Could we automatically select in Chimera-X all (residues?) lipids that cross the membrane back and forth ?
Yours sincerely
Enrico
Il giorno mer 6 nov 2024 alle ore 22:20 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: Not really, other than hiding them entirely.
Of course you could just make a separate model that contains one frame and have them sit there without moving, but that seems like it would be misleading.
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 Nov 6, 2024, at 11:35 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
I am visualizing an MD trajectory of a biomembrane system obtained from Amber MD using the autoimage method of cpptraj. However, in this trajectory, I still observe very rapid lateral diffusion of certain lipids, which cross the entire system too quickly. Is there a way in ChimeraX to hide or suppress such motions for selected atomic groups (e.g., lipids)?
Many thanks in advance
Enrico
Hi Enrico, So that others might be able to benefit without spelunking into this mailing list's archives, I've made a ChimeraX script that selects residues that cross periodic boundaries during the course of a simulation and have put in it the ChimeraX Recipes. You can find it here: Select residues that cross periodic box faces | ChimeraX Recipes <https://rbvi.github.io/chimerax-recipes/box_crossers/box_crossers.html>. --Eric
On Nov 8, 2024, at 5:39 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much for this suggestion, Elaine! In the described bilayer system visualization, we’re encountering an issue related to periodic boundary conditions (PBC). Specifically, when lipids cross the boundary, they disappear from one side (e.g., the bottom) and reappear on the opposite side (e.g., the top). While this isn’t particularly noticeable in the default representation, switching to the surface representation of lipids, reveals a significant visual artifact: lipids that cross boundaries appear to jump across the entire box in the lateral direction.
It would be great if Eric could help us out here—perhaps with a custom Python solution to clean up the visualization and smooth out the situation.
Yours with thanks
Enrico
Il giorno gio 7 nov 2024 alle ore 17:26 Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> ha scritto:
There is no way to automatically select what crosses. Of course, if you know their residue numbers and/or residue names you would use the usual way to specify them directly.
Elaine
On Nov 7, 2024, at 12:31 AM, Enrico Martinez <jmsstarlight@gmail.com <mailto:jmsstarlight@gmail.com>> wrote:
Thank you very much Elaine !
Could we automatically select in Chimera-X all (residues?) lipids that cross the membrane back and forth ?
Yours sincerely
Enrico
Il giorno mer 6 nov 2024 alle ore 22:20 Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> ha scritto: Not really, other than hiding them entirely.
Of course you could just make a separate model that contains one frame and have them sit there without moving, but that seems like it would be misleading.
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 Nov 6, 2024, at 11:35 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear Chimera-X users !
I am visualizing an MD trajectory of a biomembrane system obtained from Amber MD using the autoimage method of cpptraj. However, in this trajectory, I still observe very rapid lateral diffusion of certain lipids, which cross the entire system too quickly. Is there a way in ChimeraX to hide or suppress such motions for selected atomic groups (e.g., lipids)?
Many thanks in advance
Enrico
Thank you very much, Eric ! I've just tested the script and ran it in the same way, like smoothMD: although it appeared to load correctly, it ultimately didn't make any selections. I'm working with a quite complex membrane system, and I'm noticing that the lipids at the edges are frequently shifting positions outside the box, which is quite noticeable as a very quick jump in the visualization... One more general question: If I represent the lipids as a surface and then manually select and hide the lipids that exhibit jumping behavior, I’ve noticed that neighboring lipids appear to have gaps in their surface where they overlapped with the hidden lipids. Is there a way to refresh or update the representation to restore the complete surface of the remaining lipids? Many thanks in advance Enrico Il giorno sab 9 nov 2024 alle ore 02:04 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:
Hi Enrico, So that others might be able to benefit without spelunking into this mailing list's archives, I've made a ChimeraX script that selects residues that cross periodic boundaries during the course of a simulation and have put in it the ChimeraX Recipes. You can find it here: Select residues that cross periodic box faces | ChimeraX Recipes <https://rbvi.github.io/chimerax-recipes/box_crossers/box_crossers.html>.
--Eric
On Nov 8, 2024, at 5:39 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much for this suggestion, Elaine!
In the described bilayer system visualization, we’re encountering an issue related to periodic boundary conditions (PBC). Specifically, when lipids cross the boundary, they disappear from one side (e.g., the bottom) and reappear on the opposite side (e.g., the top). While this isn’t particularly noticeable in the default representation, switching to the surface representation of lipids, reveals a significant visual artifact: lipids that cross boundaries appear to jump across the entire box in the lateral direction.
It would be great if Eric could help us out here—perhaps with a custom Python solution to clean up the visualization and smooth out the situation.
Yours with thanks
Enrico
Il giorno gio 7 nov 2024 alle ore 17:26 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
There is no way to automatically select what crosses. Of course, if you know their residue numbers and/or residue names you would use the usual way to specify them directly.
Elaine
On Nov 7, 2024, at 12:31 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much Elaine !
Could we automatically select in Chimera-X all (residues?) lipids that cross the membrane back and forth ?
Yours sincerely
Enrico
Il giorno mer 6 nov 2024 alle ore 22:20 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: Not really, other than hiding them entirely.
Of course you could just make a separate model that contains one frame and have them sit there without moving, but that seems like it would be misleading.
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 Nov 6, 2024, at 11:35 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
I am visualizing an MD trajectory of a biomembrane system obtained from Amber MD using the autoimage method of cpptraj. However, in this trajectory, I still observe very rapid lateral diffusion of certain lipids, which cross the entire system too quickly. Is there a way in ChimeraX to hide or suppress such motions for selected atomic groups (e.g., lipids)?
Many thanks in advance
Enrico
To guarantee enclosing some set of atoms in its own surface you probably have to use the "enclose" option of the "surface" command. However, this could be very tedious since you may then need to use a separate surface command for every lipid residue (each specified by residue number, for example). But you would have to try and see depending on your exact situation and decide whether it is worth it to you. This option is described in the surface help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#options> Elaine
On Nov 9, 2024, at 1:06 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much, Eric !
I've just tested the script and ran it in the same way, like smoothMD: although it appeared to load correctly, it ultimately didn't make any selections. I'm working with a quite complex membrane system, and I'm noticing that the lipids at the edges are frequently shifting positions outside the box, which is quite noticeable as a very quick jump in the visualization...
One more general question: If I represent the lipids as a surface and then manually select and hide the lipids that exhibit jumping behavior, I’ve noticed that neighboring lipids appear to have gaps in their surface where they overlapped with the hidden lipids. Is there a way to refresh or update the representation to restore the complete surface of the remaining lipids?
Many thanks in advance
Enrico
Il giorno sab 9 nov 2024 alle ore 02:04 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto: Hi Enrico, So that others might be able to benefit without spelunking into this mailing list's archives, I've made a ChimeraX script that selects residues that cross periodic boundaries during the course of a simulation and have put in it the ChimeraX Recipes. You can find it here: Select residues that cross periodic box faces | ChimeraX Recipes.
--Eric
On Nov 8, 2024, at 5:39 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much for this suggestion, Elaine! In the described bilayer system visualization, we’re encountering an issue related to periodic boundary conditions (PBC). Specifically, when lipids cross the boundary, they disappear from one side (e.g., the bottom) and reappear on the opposite side (e.g., the top). While this isn’t particularly noticeable in the default representation, switching to the surface representation of lipids, reveals a significant visual artifact: lipids that cross boundaries appear to jump across the entire box in the lateral direction. It would be great if Eric could help us out here—perhaps with a custom Python solution to clean up the visualization and smooth out the situation. Yours with thanks Enrico
Il giorno gio 7 nov 2024 alle ore 17:26 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: There is no way to automatically select what crosses. Of course, if you know their residue numbers and/or residue names you would use the usual way to specify them directly.
Elaine
On Nov 7, 2024, at 12:31 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much Elaine !
Could we automatically select in Chimera-X all (residues?) lipids that cross the membrane back and forth ?
Yours sincerely
Enrico
Il giorno mer 6 nov 2024 alle ore 22:20 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: Not really, other than hiding them entirely.
Of course you could just make a separate model that contains one frame and have them sit there without moving, but that seems like it would be misleading.
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 Nov 6, 2024, at 11:35 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
I am visualizing an MD trajectory of a biomembrane system obtained from Amber MD using the autoimage method of cpptraj. However, in this trajectory, I still observe very rapid lateral diffusion of certain lipids, which cross the entire system too quickly. Is there a way in ChimeraX to hide or suppress such motions for selected atomic groups (e.g., lipids)?
Many thanks in advance
Enrico
Hi Enrico, The script detects residues crossing the periodic boundary by looking for atoms whose coordinates changed by more than half the box width in a single frame. Therefore, you need to apply the script before smoothing, because the smoothing will cause the coordinates to change over several frames.— so they don't change by half the box width in any single frame. --Eric
On Nov 9, 2024, at 1:06 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much, Eric !
I've just tested the script and ran it in the same way, like smoothMD: although it appeared to load correctly, it ultimately didn't make any selections. I'm working with a quite complex membrane system, and I'm noticing that the lipids at the edges are frequently shifting positions outside the box, which is quite noticeable as a very quick jump in the visualization...
One more general question: If I represent the lipids as a surface and then manually select and hide the lipids that exhibit jumping behavior, I’ve noticed that neighboring lipids appear to have gaps in their surface where they overlapped with the hidden lipids. Is there a way to refresh or update the representation to restore the complete surface of the remaining lipids?
Many thanks in advance
Enrico
Il giorno sab 9 nov 2024 alle ore 02:04 Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> ha scritto:
Hi Enrico, So that others might be able to benefit without spelunking into this mailing list's archives, I've made a ChimeraX script that selects residues that cross periodic boundaries during the course of a simulation and have put in it the ChimeraX Recipes. You can find it here: Select residues that cross periodic box faces | ChimeraX Recipes <https://rbvi.github.io/chimerax-recipes/box_crossers/box_crossers.html>.
--Eric
On Nov 8, 2024, at 5:39 AM, Enrico Martinez <jmsstarlight@gmail.com <mailto:jmsstarlight@gmail.com>> wrote:
Thank you very much for this suggestion, Elaine! In the described bilayer system visualization, we’re encountering an issue related to periodic boundary conditions (PBC). Specifically, when lipids cross the boundary, they disappear from one side (e.g., the bottom) and reappear on the opposite side (e.g., the top). While this isn’t particularly noticeable in the default representation, switching to the surface representation of lipids, reveals a significant visual artifact: lipids that cross boundaries appear to jump across the entire box in the lateral direction.
It would be great if Eric could help us out here—perhaps with a custom Python solution to clean up the visualization and smooth out the situation.
Yours with thanks
Enrico
Il giorno gio 7 nov 2024 alle ore 17:26 Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> ha scritto:
There is no way to automatically select what crosses. Of course, if you know their residue numbers and/or residue names you would use the usual way to specify them directly.
Elaine
On Nov 7, 2024, at 12:31 AM, Enrico Martinez <jmsstarlight@gmail.com <mailto:jmsstarlight@gmail.com>> wrote:
Thank you very much Elaine !
Could we automatically select in Chimera-X all (residues?) lipids that cross the membrane back and forth ?
Yours sincerely
Enrico
Il giorno mer 6 nov 2024 alle ore 22:20 Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> ha scritto: Not really, other than hiding them entirely.
Of course you could just make a separate model that contains one frame and have them sit there without moving, but that seems like it would be misleading.
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 Nov 6, 2024, at 11:35 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear Chimera-X users !
I am visualizing an MD trajectory of a biomembrane system obtained from Amber MD using the autoimage method of cpptraj. However, in this trajectory, I still observe very rapid lateral diffusion of certain lipids, which cross the entire system too quickly. Is there a way in ChimeraX to hide or suppress such motions for selected atomic groups (e.g., lipids)?
Many thanks in advance
Enrico
Yes, it works, thank you very much Eric ! All the best Enrico Il giorno mar 12 nov 2024 alle ore 20:50 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:
Hi Enrico, The script detects residues crossing the periodic boundary by looking for atoms whose coordinates changed by more than half the box width in a single frame. Therefore, you need to apply the script before smoothing, because the smoothing will cause the coordinates to change over several frames.— so they don't change by half the box width in any single frame.
--Eric
On Nov 9, 2024, at 1:06 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much, Eric !
I've just tested the script and ran it in the same way, like smoothMD: although it appeared to load correctly, it ultimately didn't make any selections. I'm working with a quite complex membrane system, and I'm noticing that the lipids at the edges are frequently shifting positions outside the box, which is quite noticeable as a very quick jump in the visualization...
One more general question: If I represent the lipids as a surface and then manually select and hide the lipids that exhibit jumping behavior, I’ve noticed that neighboring lipids appear to have gaps in their surface where they overlapped with the hidden lipids. Is there a way to refresh or update the representation to restore the complete surface of the remaining lipids?
Many thanks in advance
Enrico
Il giorno sab 9 nov 2024 alle ore 02:04 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:
Hi Enrico, So that others might be able to benefit without spelunking into this mailing list's archives, I've made a ChimeraX script that selects residues that cross periodic boundaries during the course of a simulation and have put in it the ChimeraX Recipes. You can find it here: Select residues that cross periodic box faces | ChimeraX Recipes <https://rbvi.github.io/chimerax-recipes/box_crossers/box_crossers.html>.
--Eric
On Nov 8, 2024, at 5:39 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much for this suggestion, Elaine!
In the described bilayer system visualization, we’re encountering an issue related to periodic boundary conditions (PBC). Specifically, when lipids cross the boundary, they disappear from one side (e.g., the bottom) and reappear on the opposite side (e.g., the top). While this isn’t particularly noticeable in the default representation, switching to the surface representation of lipids, reveals a significant visual artifact: lipids that cross boundaries appear to jump across the entire box in the lateral direction.
It would be great if Eric could help us out here—perhaps with a custom Python solution to clean up the visualization and smooth out the situation.
Yours with thanks
Enrico
Il giorno gio 7 nov 2024 alle ore 17:26 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
There is no way to automatically select what crosses. Of course, if you know their residue numbers and/or residue names you would use the usual way to specify them directly.
Elaine
On Nov 7, 2024, at 12:31 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much Elaine !
Could we automatically select in Chimera-X all (residues?) lipids that cross the membrane back and forth ?
Yours sincerely
Enrico
Il giorno mer 6 nov 2024 alle ore 22:20 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: Not really, other than hiding them entirely.
Of course you could just make a separate model that contains one frame and have them sit there without moving, but that seems like it would be misleading.
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 Nov 6, 2024, at 11:35 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
I am visualizing an MD trajectory of a biomembrane system obtained from Amber MD using the autoimage method of cpptraj. However, in this trajectory, I still observe very rapid lateral diffusion of certain lipids, which cross the entire system too quickly. Is there a way in ChimeraX to hide or suppress such motions for selected atomic groups (e.g., lipids)?
Many thanks in advance
Enrico
participants (4)
-
Elaine Meng -
Enrico Martinez -
Enrique Flores -
Eric Pettersen