Labeling chains in MD simulation trajectories of a multimer
Hi All, I am interested in MD simulations of homomultimeric ion channels, which I do in GROMACS. I would like to analyze my output files with ChimeraX but I run into the following problem: The .gro output of the simulation consists of a single chain named /? in ChimeraX. When I open the file in old Chimera, it shows every chain of the original protein separately but with the same name ()
Hi Alexandra, I don't actually have access to any .gro files that have multiple chains. If you could send me an example I might be able to improve ChimeraX's behavior in that situation. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Apr 22, 2025, at 7:23 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi All, I am interested in MD simulations of homomultimeric ion channels, which I do in GROMACS. I would like to analyze my output files with ChimeraX but I run into the following problem: The .gro output of the simulation consists of a single chain named /? in ChimeraX. When I open the file in old Chimera, it shows every chain of the original protein separately but with the same name ()
_______________________________________________ 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 Eric Sorry, I have sent the unfinished mail by mistake, but you got the problem perfectly. Since I need to analyze e.g. RMSD/RMSF or H-bonds per chain, I need to have different names for the four chains. I can do it in old Chimera, because it requires a combination of a TPR and an XTC file, which will produce the correct chain names. However ChimeraX reads only the GRO file but not the TPR file, and the GRO file does not seem to have this information. I attach a sample .gro file with the following .xtc trajectory. In the .gro file, everything including protein, ions, lipids, and water is one "principal chain" without a name. I have also added the .tpr file so you can compare the result in ChimeraX and Chimera. Best Sasha -----Original Message----- From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Tuesday, April 22, 2025 7:12 PM To: Alexandra Zahradnikova Cc: ChimeraX Users Help Subject: Re: [chimerax-users] Labeling chains in MD simulation trajectories of a multimer Hi Alexandra, I don't actually have access to any .gro files that have multiple chains. If you could send me an example I might be able to improve ChimeraX's behavior in that situation. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Apr 22, 2025, at 7:23 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi All, I am interested in MD simulations of homomultimeric ion channels, which I do in GROMACS. I would like to analyze my output files with ChimeraX but I run into the following problem: The .gro output of the simulation consists of a single chain named /? in ChimeraX. When I open the file in old Chimera, it shows every chain of the original protein separately but with the same name ()
_______________________________________________ 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 Alexandra, Thanks for the example file. I have committed changes to .gro file reading to do a better job of identifying chains and assigning chain IDs. In your example file, the four protein chains are assigned chain IDs A-D and all the singleton residues get chain ID E. The fix will be in the next daily build. --Eric
On Apr 22, 2025, at 1:01 PM, Alexandra Zahradnikova <Alexandra.Zahradnikova@savba.sk> wrote:
Hi Eric Sorry, I have sent the unfinished mail by mistake, but you got the problem perfectly. Since I need to analyze e.g. RMSD/RMSF or H-bonds per chain, I need to have different names for the four chains. I can do it in old Chimera, because it requires a combination of a TPR and an XTC file, which will produce the correct chain names. However ChimeraX reads only the GRO file but not the TPR file, and the GRO file does not seem to have this information. I attach a sample .gro file with the following .xtc trajectory. In the .gro file, everything including protein, ions, lipids, and water is one "principal chain" without a name. I have also added the .tpr file so you can compare the result in ChimeraX and Chimera. Best Sasha
-----Original Message----- From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Tuesday, April 22, 2025 7:12 PM To: Alexandra Zahradnikova Cc: ChimeraX Users Help Subject: Re: [chimerax-users] Labeling chains in MD simulation trajectories of a multimer
Hi Alexandra, I don't actually have access to any .gro files that have multiple chains. If you could send me an example I might be able to improve ChimeraX's behavior in that situation.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Apr 22, 2025, at 7:23 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi All, I am interested in MD simulations of homomultimeric ion channels, which I do in GROMACS. I would like to analyze my output files with ChimeraX but I run into the following problem: The .gro output of the simulation consists of a single chain named /? in ChimeraX. When I open the file in old Chimera, it shows every chain of the original protein separately but with the same name ()
_______________________________________________ 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/ <step7_1.zip>
Hi Eric thank you for your help, I will test the new build of Chimera ASAP. Best Sasha -----Original Message----- From: Eric <pett@cgl.ucsf.edu> To: Alexandra <Alexandra.Zahradnikova@savba.sk> Cc: ChimeraX <chimerax-users@cgl.ucsf.edu> Date: Thursday, 24 April 2025 2:28 AM CEST Subject: Re: [chimerax-users] Labeling chains in MD simulation trajectories of a multimer Hi Alexandra, Thanks for the example file. I have committed changes to .gro file reading to do a better job of identifying chains and assigning chain IDs. In your example file, the four protein chains are assigned chain IDs A-D and all the singleton residues get chain ID E. The fix will be in the next daily build. --Eric
On Apr 22, 2025, at 1:01 PM, Alexandra Zahradnikova <Alexandra.Zahradnikova@savba.sk> wrote:
Hi Eric Sorry, I have sent the unfinished mail by mistake, but you got the problem perfectly. Since I need to analyze e.g. RMSD/RMSF or H-bonds per chain, I need to have different names for the four chains. I can do it in old Chimera, because it requires a combination of a TPR and an XTC file, which will produce the correct chain names. However ChimeraX reads only the GRO file but not the TPR file, and the GRO file does not seem to have this information. I attach a sample .gro file with the following .xtc trajectory. In the .gro file, everything including protein, ions, lipids, and water is one "principal chain" without a name. I have also added the .tpr file so you can compare the result in ChimeraX and Chimera. Best Sasha
-----Original Message----- From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Tuesday, April 22, 2025 7:12 PM To: Alexandra Zahradnikova Cc: ChimeraX Users Help Subject: Re: [chimerax-users] Labeling chains in MD simulation trajectories of a multimer
Hi Alexandra, I don't actually have access to any .gro files that have multiple chains. If you could send me an example I might be able to improve ChimeraX's behavior in that situation.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Apr 22, 2025, at 7:23 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi All, I am interested in MD simulations of homomultimeric ion channels, which I do in GROMACS. I would like to analyze my output files with ChimeraX but I run into the following problem: The .gro output of the simulation consists of a single chain named /? in ChimeraX. When I open the file in old Chimera, it shows every chain of the original protein separately but with the same name ()
_______________________________________________ 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/ <step7_1.zip>
Hi Eric, in the new build, the chains are now correctly labeled. Thank you very much! Best Sasha -----Original Message----- From: Alexandra <Alexandra.Zahradnikova@savba.sk> To: chimerax-users <chimerax-users@cgl.ucsf.edu> Date: Thursday, 24 April 2025 11:12 AM CEST Subject: Re: [chimerax-users] Labeling chains in MD simulation trajectories of a multimer Hi Eric thank you for your help, I will test the new build of Chimera ASAP. Best Sasha -----Original Message----- From: Eric <pett@cgl.ucsf.edu> To: Alexandra <Alexandra.Zahradnikova@savba.sk> Cc: ChimeraX <chimerax-users@cgl.ucsf.edu> Date: Thursday, 24 April 2025 2:28 AM CEST Subject: Re: [chimerax-users] Labeling chains in MD simulation trajectories of a multimer Hi Alexandra, Thanks for the example file. I have committed changes to .gro file reading to do a better job of identifying chains and assigning chain IDs. In your example file, the four protein chains are assigned chain IDs A-D and all the singleton residues get chain ID E. The fix will be in the next daily build. --Eric
On Apr 22, 2025, at 1:01 PM, Alexandra Zahradnikova <Alexandra.Zahradnikova@savba.sk> wrote:
Hi Eric Sorry, I have sent the unfinished mail by mistake, but you got the problem perfectly. Since I need to analyze e.g. RMSD/RMSF or H-bonds per chain, I need to have different names for the four chains. I can do it in old Chimera, because it requires a combination of a TPR and an XTC file, which will produce the correct chain names. However ChimeraX reads only the GRO file but not the TPR file, and the GRO file does not seem to have this information. I attach a sample .gro file with the following .xtc trajectory. In the .gro file, everything including protein, ions, lipids, and water is one "principal chain" without a name. I have also added the .tpr file so you can compare the result in ChimeraX and Chimera. Best Sasha
-----Original Message----- From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Tuesday, April 22, 2025 7:12 PM To: Alexandra Zahradnikova Cc: ChimeraX Users Help Subject: Re: [chimerax-users] Labeling chains in MD simulation trajectories of a multimer
Hi Alexandra, I don't actually have access to any .gro files that have multiple chains. If you could send me an example I might be able to improve ChimeraX's behavior in that situation.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Apr 22, 2025, at 7:23 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi All, I am interested in MD simulations of homomultimeric ion channels, which I do in GROMACS. I would like to analyze my output files with ChimeraX but I run into the following problem: The .gro output of the simulation consists of a single chain named /? in ChimeraX. When I open the file in old Chimera, it shows every chain of the original protein separately but with the same name ()
_______________________________________________ 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/ <step7_1.zip>
Glad to hear it! --Eric
On Apr 24, 2025, at 6:25 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Eric, in the new build, the chains are now correctly labeled. Thank you very much! Best Sasha
-----Original Message----- From: Alexandra <Alexandra.Zahradnikova@savba.sk> To: chimerax-users <chimerax-users@cgl.ucsf.edu> Date: Thursday, 24 April 2025 11:12 AM CEST Subject: Re: [chimerax-users] Labeling chains in MD simulation trajectories of a multimer
Hi Eric thank you for your help, I will test the new build of Chimera ASAP. Best Sasha
-----Original Message----- From: Eric <pett@cgl.ucsf.edu> To: Alexandra <Alexandra.Zahradnikova@savba.sk> Cc: ChimeraX <chimerax-users@cgl.ucsf.edu> Date: Thursday, 24 April 2025 2:28 AM CEST Subject: Re: [chimerax-users] Labeling chains in MD simulation trajectories of a multimer
Hi Alexandra, Thanks for the example file. I have committed changes to .gro file reading to do a better job of identifying chains and assigning chain IDs. In your example file, the four protein chains are assigned chain IDs A-D and all the singleton residues get chain ID E. The fix will be in the next daily build.
--Eric
On Apr 22, 2025, at 1:01 PM, Alexandra Zahradnikova <Alexandra.Zahradnikova@savba.sk> wrote:
Hi Eric Sorry, I have sent the unfinished mail by mistake, but you got the problem perfectly. Since I need to analyze e.g. RMSD/RMSF or H-bonds per chain, I need to have different names for the four chains. I can do it in old Chimera, because it requires a combination of a TPR and an XTC file, which will produce the correct chain names. However ChimeraX reads only the GRO file but not the TPR file, and the GRO file does not seem to have this information. I attach a sample .gro file with the following .xtc trajectory. In the .gro file, everything including protein, ions, lipids, and water is one "principal chain" without a name. I have also added the .tpr file so you can compare the result in ChimeraX and Chimera. Best Sasha
-----Original Message----- From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Tuesday, April 22, 2025 7:12 PM To: Alexandra Zahradnikova Cc: ChimeraX Users Help Subject: Re: [chimerax-users] Labeling chains in MD simulation trajectories of a multimer
Hi Alexandra, I don't actually have access to any .gro files that have multiple chains. If you could send me an example I might be able to improve ChimeraX's behavior in that situation.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Apr 22, 2025, at 7:23 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi All, I am interested in MD simulations of homomultimeric ion channels, which I do in GROMACS. I would like to analyze my output files with ChimeraX but I run into the following problem: The .gro output of the simulation consists of a single chain named /? in ChimeraX. When I open the file in old Chimera, it shows every chain of the original protein separately but with the same name ()
_______________________________________________ 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/ <step7_1.zip>
_______________________________________________ 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/
participants (3)
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Alexandra Zahradnikova -
Alexandra Zahradnikova
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Eric Pettersen