Dear All, I am new in molecular simulation and not very much experienced with ChimeraX. I did not find an easy way to concatenate trajectories (in my case, .xtc files from gromacs). Any suggestions would be welcome. Thanks in advance Sasha ________________________________________________________________________ Alexandra Zahradníková, PhD Department of Cell Cardiology Institute of Experimental Endocrinology Biomedical Research Centre SAS Dúbravská cesta 9 845 05 Bratislava Slovakia Mobile: +421 908 069 796
Hi Sasha, You have to use the “open” command to do this (not the Open→File dialog). With the command, add the option “replace false” to append the frames to the existing ones instead of replacing them, --Eric Eric Pettersen UCSF Computer Graphics Lab
On Mar 28, 2025, at 8:05 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear All, I am new in molecular simulation and not very much experienced with ChimeraX. I did not find an easy way to concatenate trajectories (in my case, .xtc files from gromacs). Any suggestions would be welcome. Thanks in advance Sasha ________________________________________________________________________ Alexandra Zahradníková, PhD Department of Cell Cardiology Institute of Experimental Endocrinology Biomedical Research Centre SAS Dúbravská cesta 9 845 05 Bratislava Slovakia Mobile: +421 908 069 796
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Dear Eric thank you for your help. I see now that the information is in the ChimeraX help files under "open" but I was looking under "trajectory" so I was not able to find it. Best Sasha -----Original Message----- From: Eric <pett@cgl.ucsf.edu> To: Alexandra <alexandra.zahradnikova@savba.sk> Cc: chimerax-users <chimerax-users@cgl.ucsf.edu> Date: Tuesday, 1 April 2025 12:53 AM CEST Subject: Re: [chimerax-users] Concatenating trajectories in ChimeraX Hi Sasha, You have to use the “open” command to do this (not the Open→File dialog). With the command, add the option “replace false” to append the frames to the existing ones instead of replacing them, --Eric Eric Pettersen UCSF Computer Graphics Lab On Mar 28, 2025, at 8:05 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Dear All, I am new in molecular simulation and not very much experienced with ChimeraX. I did not find an easy way to concatenate trajectories (in my case, .xtc files from gromacs). Any suggestions would be welcome. Thanks in advance Sasha ________________________________________________________________________ Alexandra Zahradníková, PhD Department of Cell Cardiology Institute of Experimental Endocrinology Biomedical Research Centre SAS Dúbravská cesta 9 845 05 Bratislava Slovakia Mobile: +421 908 069 796 _______________________________________________ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.eduTo unsubscribe send an email to chimerax-users-leave@cgl.ucsf.eduArchives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Dear All, dear Eric, After concatenating the trajectories, I noticed that the last frame of the (i-1)-th trajectory file (in xtc format) and the 1st frame of the i-th trajectory file are identical. Is it possible to remove this duplication? Best regards Sasha From: Alexandra Zahradnikova [mailto:Alexandra.Zahradnikova@savba.sk] Sent: Wednesday, April 2, 2025 10:02 AM To: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Concatenating trajectories in ChimeraX Dear Eric thank you for your help. I see now that the information is in the ChimeraX help files under "open" but I was looking under "trajectory" so I was not able to find it. Best Sasha _____ From: Eric <pett@cgl.ucsf.edu> To: Alexandra <http://alexandra.zahradnikova@savba.sk> Cc: chimerax-users <chimerax-users@cgl.ucsf.edu> Date: Tuesday, 1 April 2025 12:53 AM CEST Subject: Re: [chimerax-users] Concatenating trajectories in ChimeraX Hi Sasha, You have to use the “open” command to do this (not the Open→File dialog). With the command, add the option “replace false” to append the frames to the existing ones instead of replacing them, --Eric Eric Pettersen UCSF Computer Graphics Lab On Mar 28, 2025, at 8:05 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Dear All, I am new in molecular simulation and not very much experienced with ChimeraX. I did not find an easy way to concatenate trajectories (in my case, .xtc files from gromacs). Any suggestions would be welcome. Thanks in advance Sasha ________________________________________________________________________ Alexandra Zahradníková, PhD Department of Cell Cardiology Institute of Experimental Endocrinology Biomedical Research Centre SAS Dúbravská cesta 9 845 05 Bratislava Slovakia Mobile: +421 908 069 796 _______________________________________________ ChimeraX-users mailing list -- <mailto:chimerax-users@cgl.ucsf.edu> chimerax-users@cgl.ucsf.edu To unsubscribe send an email to <mailto:chimerax-users-leave@cgl.ucsf.edu> chimerax-users-leave@cgl.ucsf.edu Archives: <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/
Hi Sasha, The "open" command trajectory options include "start" and "end" for specifying which part of the trajectory to load. So when loading the second part, maybe you can use "start 2" to skip the first frame. See the "open" command trajectory options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#traj-options> 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 Apr 18, 2025, at 4:06 PM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear All, dear Eric, After concatenating the trajectories, I noticed that the last frame of the (i-1)-th trajectory file (in xtc format) and the 1st frame of the i-th trajectory file are identical. Is it possible to remove this duplication? Best regards Sasha From: Alexandra Zahradnikova [mailto:Alexandra.Zahradnikova@savba.sk] Sent: Wednesday, April 2, 2025 10:02 AM To: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Concatenating trajectories in ChimeraX Dear Eric thank you for your help. I see now that the information is in the ChimeraX help files under "open" but I was looking under "trajectory" so I was not able to find it. Best Sasha
From: Eric <pett@cgl.ucsf.edu> To: Alexandra <alexandra.zahradnikova@savba.sk> Cc: chimerax-users <chimerax-users@cgl.ucsf.edu> Date: Tuesday, 1 April 2025 12:53 AM CEST Subject: Re: [chimerax-users] Concatenating trajectories in ChimeraX
Hi Sasha, You have to use the “open” command to do this (not the Open→File dialog). With the command, add the option “replace false” to append the frames to the existing ones instead of replacing them, --Eric Eric Pettersen UCSF Computer Graphics Lab
On Mar 28, 2025, at 8:05 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Dear All, I am new in molecular simulation and not very much experienced with ChimeraX. I did not find an easy way to concatenate trajectories (in my case, .xtc files from gromacs). Any suggestions would be welcome. Thanks in advance Sasha
participants (4)
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Alexandra Zahradnikova -
Alexandra Zahradnikova
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Elaine Meng -
Eric Pettersen