rendering of bond making/breaking along a trajectory
Hi, I am not sure whether this is a bug or something not yet implemented or else. I performed QM/MM simulations of a proton translocating along a water chain. This involves the breaking of a bond and the making of a new bond. The visualization of the trajectory does not show this process; instead, the original definition of bond is retained, without being updated at each timeframe. Is there a way to tell ChimeraX to automatically check covalent bonds at each snapshot and update the bond accordingly? A simple distance criterion will do. This is only for rendering purpose. In case further clarifications are needed: D—H.......A (with -- indicating the covalent bond between proton and domor and .... indicating the proximal acceptor) must be transformed to D.......H—A. Instead, it is rendered as D-------H..A (with an artificially elongated DH bond and no new HA bond) thanks s _____________________________________ Sergio A. Hassan https://bioinformatics.niaid.nih.gov/cmm/ BCBB/NIAID/NIH/DHHS 301 761 7221 (office) 301 741 5579 (mobile)
Hi Sergio, I wouldn't call it a bug, just that the assumption for a trajectory or other ensemble (e.g. from NMR) is that it has the same atoms and bonds at each frame. However, you can destroy and re-guess bonds at each frame, with some possible hit on live playback speed, as described in this recent chimerax-users post: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-April/005164.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 13, 2023, at 9:24 AM, Hassan, Sergio (NIH/NIAID) [E] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I am not sure whether this is a bug or something not yet implemented or else.
I performed QM/MM simulations of a proton translocating along a water chain. This involves the breaking of a bond and the making of a new bond. The visualization of the trajectory does not show this process; instead, the original definition of bond is retained, without being updated at each timeframe.
Is there a way to tell ChimeraX to automatically check covalent bonds at each snapshot and update the bond accordingly? A simple distance criterion will do. This is only for rendering purpose.
In case further clarifications are needed: D—H.......A (with -- indicating the covalent bond between proton and domor and .... indicating the proximal acceptor) must be transformed to D.......H—A. Instead, it is rendered as D-------H..A (with an artificially elongated DH bond and no new HA bond)
thanks s
Thank you, Elaine, I'll check that path, Best _____________________________________ Sergio A. Hassan https://bioinformatics.niaid.nih.gov/cmm/ BCBB/NIAID/NIH/DHHS 301 761 7221 (office) 301 741 5579 (mobile) ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, May 15, 2023 2:25 PM To: Hassan, Sergio (NIH/NIAID) [E] <hassan@mail.nih.gov> Cc: Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Subject: [EXTERNAL] Re: [chimerax-users] rendering of bond making/breaking along a trajectory Hi Sergio, I wouldn't call it a bug, just that the assumption for a trajectory or other ensemble (e.g. from NMR) is that it has the same atoms and bonds at each frame. However, you can destroy and re-guess bonds at each frame, with some possible hit on live playback speed, as described in this recent chimerax-users post: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fpipermail%2Fchimerax-users%2F2023-April%2F005164.html&data=05%7C01%7Chassan%40mail.nih.gov%7C1b4ea0b92345462253f208db5571c60c%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638197719374440268%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=E4P6A3V8R6Myc0fGybd9jzR92ERH0%2BVkzjlWANn8eTk%3D&reserved=0<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-April/005164.html>> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 13, 2023, at 9:24 AM, Hassan, Sergio (NIH/NIAID) [E] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I am not sure whether this is a bug or something not yet implemented or else.
I performed QM/MM simulations of a proton translocating along a water chain. This involves the breaking of a bond and the making of a new bond. The visualization of the trajectory does not show this process; instead, the original definition of bond is retained, without being updated at each timeframe.
Is there a way to tell ChimeraX to automatically check covalent bonds at each snapshot and update the bond accordingly? A simple distance criterion will do. This is only for rendering purpose.
In case further clarifications are needed: D—H.......A (with -- indicating the covalent bond between proton and domor and .... indicating the proximal acceptor) must be transformed to D.......H—A. Instead, it is rendered as D-------H..A (with an artificially elongated DH bond and no new HA bond)
thanks s
CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.
Elaine, Just to confirm that your suggestion about using the 'perframe' command worked beautifully. Thanks again s _____________________________________ Sergio A. Hassan https://bioinformatics.niaid.nih.gov/cmm/ BCBB/NIAID/NIH/DHHS 301 761 7221 (office) 301 741 5579 (mobile) ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, May 15, 2023 2:25 PM To: Hassan, Sergio (NIH/NIAID) [E] <hassan@mail.nih.gov> Cc: Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Subject: [EXTERNAL] Re: [chimerax-users] rendering of bond making/breaking along a trajectory Hi Sergio, I wouldn't call it a bug, just that the assumption for a trajectory or other ensemble (e.g. from NMR) is that it has the same atoms and bonds at each frame. However, you can destroy and re-guess bonds at each frame, with some possible hit on live playback speed, as described in this recent chimerax-users post: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fpipermail%2Fchimerax-users%2F2023-April%2F005164.html&data=05%7C01%7Chassan%40mail.nih.gov%7C1b4ea0b92345462253f208db5571c60c%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638197719374440268%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=E4P6A3V8R6Myc0fGybd9jzR92ERH0%2BVkzjlWANn8eTk%3D&reserved=0<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-April/005164.html>> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 13, 2023, at 9:24 AM, Hassan, Sergio (NIH/NIAID) [E] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I am not sure whether this is a bug or something not yet implemented or else.
I performed QM/MM simulations of a proton translocating along a water chain. This involves the breaking of a bond and the making of a new bond. The visualization of the trajectory does not show this process; instead, the original definition of bond is retained, without being updated at each timeframe.
Is there a way to tell ChimeraX to automatically check covalent bonds at each snapshot and update the bond accordingly? A simple distance criterion will do. This is only for rendering purpose.
In case further clarifications are needed: D—H.......A (with -- indicating the covalent bond between proton and domor and .... indicating the proximal acceptor) must be transformed to D.......H—A. Instead, it is rendered as D-------H..A (with an artificially elongated DH bond and no new HA bond)
thanks s
CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.
participants (2)
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Elaine Meng -
Hassan, Sergio (NIH/NIAID) [E]